To explore the mechanism of pigment content and cell structure on the flower color formation of Michelia crassipes, we determined the content of pigment and cell ultrastructural in its perianth during 2 different colors. The relationship between pigment content and color formation of perianth was analyzed by stepwise regression equation, and the ultrastructural changes of tepals were observed by paraffin section and ultrathin section technology. The results showed that: (1) the L^* values of purple perianth surface were decreased, as did the b^* values, but the a^* values were enhanced. The accumulation of anthocyanins and the increase of carotenoids and flavonoids in perianth were accompanied by the degradation and decrease of chlorophyll content. (2) a^* was positively correlated with the content of anthocyanins, flavonoids, carotenoids and anthocyanins/flavonoids, anthocyanins/chlorophyll, while b^* was positively correlated with chlorophyll content and anthocyanins/carotenoids; (3) in cellular structure, as the perianth turns from green to purple, upper epidermal cells change from flat to conical protrusions, lengthwidth ratio increases and anticlinal walls folds. The epidermal structure of purple perianth absorbed more incident light and the increase of vacuole area and the transformation of chloroplasts into chromoplasts were the main organelle changes. It was found that the coloration of perianth was the result of many factors. The generation and accumulation of anthocyanin content and the increase of carotenoid and flavonoid content may be the main reasons for the purple color of M. crassipes, with the ultrastructure shows that the vacuole area increased and chloroplast transformed into plasmid.