Chinese cabbage Sclerotinia rot is caused by Sclerotinia sclerotiorum, which seriously endangers the yield and quality of Chinese cabbage. In this study, the transcription level of resistance genes to the infection of S. sclerotiorum were explored at the molecular level and provided candidate genes for further study of disease resistance mechanism. The leaves of resistant inbred line H72 and susceptible strain Y26 were inoculated for transcriptome sequencing analysis. The results show that a total of 121.77 Gb clean reads were obtained by transcriptome sequencing analysis. Filtering the raw sequencing data, the clean reads of each sample were over 6 Gb, Q₂₀ ranged from 97.21% to 97.99%, and the average percentage was 97.61%, Q₃₀ ranged from 92.59% to 93.98%%, and the average percentage was 93.20%, indicating that the sequencing quality could be used for subsequent analysis. The number of common differentially expressed genes were 13 and 11 after inoculation for 36 h and 48 h, respectively. After removing the common differentially expressed genes at each time point, we obtained 18 differentially expressed genes. Combined with gene function annotation, 11 genes involved in defense response. MYB34 transcription factor was up-regulated, while ERF003 was down-regulated, which might negatively regulate the infection of S. sclerotiorum. Gretchen hagen 3.3 (GH3.3), PR proteins (TLP1), F-box, amino acid transporter (ANT1), caffeoyl-CoA O-methyltransferase (Cco AOMT), aspartyl protease (AED3), chaperone protein (DnaJ 11) were up-regulated, which were proposed to response to Chinese cabbage pathogen. The expression of epithiospecifier protein (ESP) and calcineurin B-like protein gene (CBL1) were down-regulated, and the disease resistance function in Chinese cabbage needs further analysis and verification. A further qPCR analysis was used to verify the transcriptome, The expression trends of differentially expressed genes ERF003, CBL1, GH3.3, MYB34, ANT1, TLP1 were consistent with that of transcriptome sequencing. These results will be helpful for further research the resistance mechanism to S. sclerotiorum.