In this study， untargeted metabolomics method was used to detect and analysis the differences of metabolites during the development of brownspot at storage stage. Sweet orange fruit were used as experimental materialsl， and their metabolic compounds were detected and analyzed by sample repetitive correlation analysis， cluster analysis， partial least squares discriminant analysis(PLS-DA) and KEGG pathway based on the high-performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS) instrument platform. The results showed that brownspot was significantly inhibited by PE packaging treatment. A total of 1 191 metabolites were identified in citrus fruit. In the CK-42 d vs CK-0 d samples， a total of 107 significantly different metabolites were detected， which 62 metabolic compounds were significantly up-regulated and 45 metabolic compounds were significantly down-regulated. While in the PE-42 d vs CK-0 d sample， a total of 124 significantly different metabolites were identified. Among them， 65 compounds were significantly up-regulated and 59 compounds were significantly down-regulated. The different metabolic compounds mainly distributed in 10 KEGG metabolic pathways， the first top 3 pathways are global and overview maps， amino acid metabolism and biosynthesis of other secondary metabolites. While the different metabolic compounds mainly distributed in 11 HMDB metabolic pathways， the first top 5 pathways are phenylpropanoids and polyketides， lipids and lipid-like molecules， organoheterocyclic compounds， organic acids and derivatives and benzenoids biosynthesis. These results are helpful to improve the formation mechanism of peel pitting， and can provide a reference for improving the preservation effect of citrus fruit.