Carotenoids are one of the important coloring substances in the ray florets of Zinnia elegans. Carotenoid cleavage dioxygenase (CCD) directly affects carotenoid contents by cleaving the double bond of carotenoids, thereby affecting the flower color. However, few reports have elucidated its function in Zinnia elegans. In the present study, through transcriptome homology searches, three ZeCCDs, ZeCCD1, ZeCCD4-1, and ZeCCD4-2 were screened from Zinnia elegans. The function of ZeCCDs was verified by bacterial pigment complementation system, and it revealed that all of the three ZeCCDs had the ability to cleave β-carotene and other carotenoids (ε-carotene, zeaxanthin and lycopene). Meanwhile, the expression levels of ZeCCD1 and ZeCCD4-2 in the petals of different cultivars were significantly negatively correlated with the carotenoid content. Furthermore, compared with the cytoplasmic localization of ZeCCD1, ZeCCD4-2 is localized in the plastid. Our results indicate that ZeCCD4-2 is the key gene responsible for the differential accumulation of carotenoids in the petals of different Zinnia elegans cultivars. This study lays a foundation for further research on the molecular mechanism of petal coloration and carotenoid metabolism of Zinnia elegans.