To investigate the effect of bagging on the fruit quality of ‘Honghuayingzui’ peach, gas chromatography-tandem mass spectrometry (GC-MS/MS) was used to analyze the metabolite profiles of bagged and unbagged peach fruits. The results showed a total of 634 metabolites were identified, including 11 sugars, 33 free fatty acids, and 590 volatile compounds. Among these, 107 significantly differential metabolites were identified, including 59 up-regulated substances and 48 down-regulated substances. Compared with the non-bagged group, the bagged fruit exhibited improved appearance quality and significantly reduced contents of sorbitol and oleic acid (P < 0.05). Additionally, the bagged fruit had a greater diversity of volatile compounds, with a weakened green aroma but enhanced floral, fruity and sweet aromas. However, no significant differences (P > 0.05) were observed in sweetness, total sugar, total free fatty acid, or total volatile compound contents. This study provides an important theoretical basis for improving the quality of bagged peach fruit.