Efficient photosynthesis is critical for plant survival and growth. When plant-absorbed light exceeds the overall rate of energy conversion, it will trigger photooxidation. In this study, we selected a photooxidation mutant 812HS, it was isolated from the progeny of japonica rice ( Oryza sativa L.) 812S and shows leaf yellowing and hypersensitive to photooxidation. Chloroplast ultrastructure in the leaves of 812HS showed that photooxidation resulted in significant chloroplast damage compared with 812S for changes in gene expressions in response to photooxidation stress using next-generation sequencing technologies on an Illumina HiSeq 2000 platform. A total of 88508 and 88495 genes were identified from 812S and 812HS, respectively. Expressions of 1199 genes were significantly upregulated, while 1342 genes were remarkably downregulated in 812HS. These genes were notably enriched in the 21 KEGG pathways. Based on their expression patterns, several key pathways were identified to be involved in the photooxidation of 812HS. qRT-PCR analysis further confirmed the results of RNA-Seq. This study enabled us to integrate analysis of RNA-Seq in rice and offered a deeper insight into the molecular mechanisms in response to photo-oxidative stress and provided clues for further critical gene identification in the protective mechanisms against photooxidation.