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GF-6 is the first optical remote sensing satellite for precision agriculture observations in China. Accurate identification of the cloud in GF-6 helps improve data availability. However, due to the narrow band range contained in GF-6, Fmask version 3.2 for Landsat is not suitable for GF-6. Hence, this paper proposes an improved Fmask based on the spectral-contextual information to solve the inapplicability of Fmask version 3.2 in GF-6. The improvements are divided into the following six aspects. The shortwave infrared (SWIR) in the “Basic Test” is replaced by blue band. The threshold in the original “HOT Test” is modified based on the comprehensive consideration of fog and thin clouds. The bare soil and rock are detected by the relationship between green and near infrared (NIR) bands. The bright buildings are detected by the relationship between the upper and lower quartiles of blue and red bands. The stratus with high humidity and fog_W (fog over water) are distinguished by the ratio of blue and red edge position 1 bands. Temperature probability for land is replaced by the HOT-based cloud probability (LHOT), and SWIR in brightness probability is replaced by NIR. The average cloud pixels accuracy (TPR) of the improved Fmask is 95.51%.