Granulation is a serious physiological disorder in citrus fruit, which impairs the fruit quality and causes economic losses to the citrus industry. ‘Harumi’ ((Citrus unshiu × C. sinensis) × C. reticulate), a mandarin-type variety, is prone to granulation, especially after long-term storage. In the present study, to elucidate the molecular mechanism of granulation, physiochemical changes were investigated in the juice sacs of ‘Harumi’ during the granulation process. The results showed that large size fruit (L fruit, transverse diameter of 8.5 - 10.0 cm) was prone to granulation, while small size fruit (S fruit, transverse diameter of 5.0 - 6.5 cm) was not. In L fruit, lignin content increased rapidly, which was accompanied by the reduction of the content of sugars (fructose and glucose) and organic acid (citric acid) during the granulation process. Moreover, the occurrence of granulation inhibited carotenoid biosynthesis in the ‘Harumi’ fruit. In L fruit, the content of the major carotenoids, β-cryptoxanthin, all-trans-violaxanthin, and 9-cis-violaxanthin, were decreased during the granulation process, and as a result, total carotenoid content in L fruit was 75.8% lower than that in S fruit in the fifth month after harvest. The real-time PCR results showed that the expression of carotenoid biosynthetic genes (CitPSY, CitPDS, CitZDS, CitLCYb2, and CitHYb) was down-regulated, while the expression of carotenoid catabolic genes (CitNCED2 and CitNCED3) was up-regulated in L fruit during the granulation process. This study is the first to investigate the carotenoid metabolism during the granulation process, which will provide new insights into exploring the causes of granulation in citrus fruit.