Bagged flat peaches are becoming more and more popular with consumers because of their light fruit cracking, good appearance and golden or slightly reddish fruit surface. The cultivar "Zhongyoupan 9" with rapid cultivation expansion and several others can accumulate anthocyanins under bagging conditions, showing a light-insensitive anthocyanin biosynthesis pattern, though the molecular mechanism remains unclear. In the present study, we used the exocarp samples of bagged fruits of "Zhongyoupan 9" at 89 DAFB and 102 DAFB as experimental materials for transcriptomic, metabolomic and bi-omics analyses, to analyse the mechanism of light-insensitive phenotype in "Zhongyoupan 9" after bagging and shading. The results showed that a total of 2652 significant differential genes were identified by transcriptome analysis, including 16 differentially expressed genes related to anthocyanin biosynthesis, such as PpPAL, PpC4H, Pp4CLs, PpCHSs, PpCHIs, F3H, F3"H, PpDFR, PpANS, PpUFGT, PpGST, and 56 specifically up-regulated transcription factors, all of which were up-regulated and expressed in a pattern that correlated with anthocyanin content. High performance liquid tandem mass spectrometry (UPLC-MS/MS) was used to detect changes in the relative content of flavonoid metabolites in the exocarp at developmental stages, and a total of 112 significantly different metabolites were detected, with a significant up-regulation of cyanidin-3,5-O-diglucoside, with the highest multiplicity of difference of 16.8 in Log2FC. The continuous accumulation of cyanidin-glucoside was the main metabolite responsible for the red colour of the exocarp after bagging of "Zhongyoupan 9". The results of co-analysis with KEGG enrichment analysis indicated that the up-regulated expression of transcription factors PpBL and PpNAC1 activated the expression of PpMYB10.1 under bagging and shading, which promotes the catalytic synthesis of the anthocyanin biosynthesis structural genes to synthesise cyanidin-3,5-O-diglucoside, which results in red colouration of the exocarp. The project"s progression holds not only theoretical significance but also substantial practical value, as its findings will contribute to unraveling the molecular mechanism of anthocyanin accumulation in peach fruits under bagging, providing a theoretical basis for selecting more suitable peach varieties for bagging cultivation.