A new type of japonica photo(thermo)sensitive cytoplasmic male sterile line 2310SA was bred. This line contains photo（thermo）sensitive genic male sterile（PTGMS） genes in the twoline system hybrid rice and cytoplasmic male sterile (CMS) genes in the threeline system hybrid rice, which has a great application potential in hybrid rice breeding for its stable sterility. To understand the underlying genetic mechanism and to explore male sterility of rice, the selected 2310SA line and its maintainer line of the twoline system, PTGMS line 2310S, were grown in Hefei, China. The anthers were collected at four panicle developmental stages (meiosis, mononucleate, binucleate and mature stages) and the isolated RNA were used for microarray analysis. Results showed that differentially expressed genes(DEGs) at meiosis stage(1938 genes upregulated, 1635 genes downregulated) and mature stage(2220 genes upregulated，2656 genes downregulated) were more than those at mononucleate stage(752 genes upregulated, 693 genes downregulated) and binucleate stage(1025 genes upregulated, 886 genes downregulated). The number of downregulated genes was higher than that of upregulated genes at mature stage, whereas at other stages the number of upregulated genes was more than that of downregulated genes. Moreover, hierarchical cluster analysis of all DEGs suggested that the expression of the DEGs at mononucleate and binucleate stages belonged to the same cluster, and the expression of the DEGs at meiosis and mature stages to another two clusters. Among DEGs, 147 genes were found to be differentially expressed at all the stages when comparing 2310SA line with the control line 2310S. For the 147 common DEGs, the downregulated genes were more than the upregulated ones at mature stage but not at other three stages. Additionally, these common DEGs were involved in many biological processes, which were classified into 11 functional categories, including biosynthesis, response to stimulus, photosynthesis, macromolecule metabolic process, signal transduction, regulation of transcription, carbohydrate metabolic process, flower development and cell death. Among proteins coded by the common DEGs, cytochrome P450 family protein and betaring hydroxylase play important roles in fatty acid metabolism, and heat shock transcription factor 29, heat shock protein DnaJ family protein and heat shock protein 70 are involved in stress response. These genes are likely to relate directly or indirectly to cell death and pollen abortion.