Combined spraying of gibberellin (GA) and prohydrojasmon (PDJ) was an effective method to reduce peel puffing in Satsuma mandarins. However, in the GA-and-PDJ combined treatment, fruit color development was delayed during the ripening process. In the present study, to improve the coloration of the GA and PDJ-treated fruit, the effects of exogenous application of 1-naphthaleneacetic acid (NAA) and abscisic acid (ABA) on chlorophyll and carotenoid accumulation were investigated. The results showed that both ABA and NAA treatments accelerated the color changes from green to orange in the GA and PDJ-treated fruit during the ripening process. With the NAA and ABA treatments, chlorophylls contents were decreased rapidly, and the contents of β,β-xanthophylls were significantly enhanced in the GA and PDJ-treated fruit. In addition, gene expression results showed that the changes of the chlorophyll and carotenoid metabolisms in the NAA and ABA treatments were highly regulated at the transcriptional level. The results presented in this study suggested that the application of NAA and ABA could potentially be used for improving the coloration of the GA and PDJ-treated fruit.