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Photoperiod and thermo-sensitive genic male sterile (PTGMS) rice is an important resource for two line hybrid rice production. The SQUAMOSA–promoter binding, such as the (<i>SPL</i>) gene family, encode the plant specific transcription factors that regulate development and defense responses in plants. However, the reports about <i>SPLs</i> participating in male fertility regulation are limited. Here, we identified 19 <i>OsSPL</i> family members and investigated their involvement in the fertility regulation of the PTGMS rice lines, PA2364S and PA2864S, with different fertility transition temperatures. The results demonstrated that <i>OsSPL2</i>, <i>OsSPL4</i>, <i>OsSPL16</i> and <i>OsSPL17</i> affect male fertility in response to temperature changes through the MiR156-<i>SPL</i> module. WGCNA (weighted gene co-expression network analysis) revealed that <i>CHI</i> and <i>APX1</i> were co-expressed with <i>OsSPL17</i>. Targeted metabolite and flavonoid biosynthetic gene expression analysis revealed that <i>OsSPL17</i> regulates the expression of flavonoid biosynthesis genes <i>CHI,</i> and the up regulation of flavanones (eriodictvol and naringenin) and flavones (apigenin and luteolin) content contributed to plant fertility. Meanwhile, <i>OsSPL17</i> negatively regulates <i>APX1</i> to affect APX (ascorbate peroxidase) activity, thereby regulating ROS (reactive oxygen species) content in the tapetum, controlling the PCD (programmed cell death) process and regulating male fertility in rice. Overall, this report highlights the potential role of <i>OsSPL</i> for the regulation of male fertility in rice and provides a new insight for the further understanding of fertility molecular mechanisms in PTGMS rice.