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Rice height, as the fundamental biophysical attribute, is a controlling factor in crop phenology estimation and yield estimation. The aim of this study was to use time series Sentinel-1A images to estimate the spatio-temporal distribution of rice height. In this study, a particle filter (PF) was applied for the real-time estimation of rice height compared with a simplified water cloud model (SWCM) on the basis of rice mapping and transplanting date. It was found that the VH backscatter (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>h</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula>) can potentially be applied to accurately estimate rice height compared with VV backscatter (<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>v</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula>), the <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>h</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula>/<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>v</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mn>0</mn></msup></semantics></math></inline-formula> ratio, and the Radar Vegetation Index (RVI, 4* <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>h</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula>/(<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>h</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula>+<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>v</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula>)). The results show that the rice height estimation by PF generated a better result with a root-mean-square error (RMSE) equal to 7.36 cm and a determination factor (R<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mn>2</mn></msup></semantics></math></inline-formula>) of 0.95 compared with SWCM (RMSE = 12.59 cm and R<inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mn>2</mn></msup></semantics></math></inline-formula> = 0.86). Moreover, rice height in the south and east of the study area was higher than in the north and west. The reason for this is that the south and east are near to the South China Sea, and there are higher temperatures and earlier transplanting. Altogether, our results demonstrate the potential of PF and <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mi>σ</mi></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msub><mrow></mrow><mrow><mi>v</mi><mi>h</mi></mrow></msub></semantics></math></inline-formula><inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><msup><mrow></mrow><mi>o</mi></msup></semantics></math></inline-formula> to study the spatio-temporal distribution of crop height estimation. As a result, the PF method can contribute greatly to improvements in crop monitoring.