Abstract: In order to clarify the molecular mechanism of sweet pepper in response to low temperature stress, the MDA content, SOD activity of sweet pepper seedlings and the relative parameters of photosynthesis under the low temperature stress were determined, and the transcriptome was sequenced and analyzed. The results showed that the content of MDA in sweet pepper increased significantly, the activity of SOD decreased significantly, and the photosynthetic relative parameters decreased significantly under the low temperature stress for 3 days. Compared with those before the treatment of low temperature, the transcriptome sequencing analysis showed that the differentially expressed genes were mainly involved in the enzyme system, photosynthesis, signal transduction and related transcription factors. Among them, the expression of SOD-related gene CaSOD was up-regulated, and the expression of photosynthesis key genes CaCP4 and CaHCR was significantly down-regulated. The results laid a foundation for the further analysis of the molecular mechanism of sweet pepper seedlings in response to the low temperature stress and the anti-low temperature breeding of sweet pepper.