Chlorophyll and carotenoid are the main pigments that are responsible for coloration of citrus fruit. The changes in their contents are related to the development stage in citrus fruit. During fruit maturation, carotenoids are massively accumulated in the flavedo and juice sacs, while the chlorophyll contents decreased rapidly. In contrast, the increase of chlorophyll content and decrease of carotenoid contents are observed in the fruit during regreening process. In addition, plant hormones and environmental conditions play important roles in the regulation of color development and the changes of chlorophyll and carotenoid contents in citrus fruit. In this review, we summarized the changes in chlorophyll and carotenoid contents in the flavedo and juice sacs of citrus fruit during fruit maturation and regreening process. Current understanding on the molecular mechanisms that regulated the chlorophyll and carotenoid metabolisms in citrus fruit are discussed. Moreover, the effects of plant hormones and environmental conditions on chlorophyll and carotenoid accumulation are also presented in this review.