Magnesium (Mg) has been found to promote the color change citrus peel, but the underlying mechanism remains unclear. In this study, Mg application treatment significantly increased the Mg content in the peel of Satsuma mandarin fruit during the expansion stage (90–150 days after flowering). Mg fertilizer treatment was also found to significantly reduce chlorophyll (Chl) a content and increase β, β-xanthophyll (β-cryptoxanthin, zeaxanthin, neoxanthin), and abscisic acid (ABA) content in the flavedo during the key period of color change in Satsuma mandarin (165–195 days after flowering). Under Mg fertilizer treatment, Chl biosynthesis genes (CitGGDR, CitCHLH, CitCHLM, CitCHL27, and CitPORA) was down-regulated and that of Chl degradation genes (CitNYC, CitPPH, CitPAO, and CitRCCR) was up-regulated, which resulted in a lower Chl content in the flavedo than the control. Moreover, Mg fertilizer treatment up-regulated carotenoid biosynthesis genes (CitPSY, CitPDS, CitZDS, CitLCYb1, CitLCYb2, CitZEP, CitNCED2, and CitNCED3), leading to the accumulation of β, β-xanthophyll and ABA in the flavedo. Mg fertilizer treatment also promoted sugar (mainly fructose, glucose, and sucrose) accumulation in fruit flavedo, which showed significant negative correlations with Chl, α-carotene, lutein, and β-carotene, but positive correlations with β, β-xanthophyll compositions, and ABA in the flavedo. An analysis integrating transcriptome and metabolome data revealed that Mg may promote the color change of Satsuma mandarin fruit flavedo by regulating various metabolic pathways related to peel coloration, such as sugar accumulation, Chl degradation, carotenoid and ABA biosynthesis, and carbon fixation. The results can explain the regulatory pathways and networks of Mg-induced citrus peel coloration.