Degreening is widely used in citrus fruit to extend the market season for economic gains and increase the consumer acceptance. Elevated CO2 was exogenously applied to Satsuma mandarins (Citrus unshiu Marc.) for degreening and its effect on pigment metabolism was investigated. The results revealed 15% CO2 treatment accelerated the citrus fruit peel color change along with the chlorophyll degradation, β-cryptoxanthin and flavonoids accumulation. The expression of CitSGR, CitNYC, CitChlase, CitPPH, CitPAO and CitRCCR genes involved in chlorophyll metabolism and a set of genes involved in producing β, β-xanthophylls were up-regulated by elevated CO2. For flavonoid metabolism, the up-regulated expressions of CitPAL, CitCHS and CitCHI partly explained the increased total flavonoids content. These results showed that 15% CO2 treatment improved the visual appearance of citrus fruits due to its impact on pigment metabolism and also maintained their nutritional value, thus could be employed as a potential commercial technique for citrus degreening.