In order to explore the formation mechanism of fruit color difference between Dahong and Wucihuanglong pitaya, the fruits at different development stages of 13 d, 16 d, 19 d, 22 d, 25 d and 28 d after fruit setting were sampled. The color parameters, total content, components and relative content change of Betalains in different parts (flesh, peel and sepal) were determined, and the results were analyzed by correlation and principal component analysis. Results showed that a^* value of Dahong flesh gradually increased and the flesh showed red color 16 days after fruit setting. The a^* value of the peel and sepal was negative before 19 d after fruit setting, positive during 19 d to 28 d and showed an upward trend; the b^* value significantly increased and then decreased after 22 d after fruit setting, showing that green first turned to red and yellow, then turned to red. The a^* value of the peel and sepal of Wucihuanglong was negative before 25 d, and the absolute value of 28 d was close to 0; the b^* value showed a stable trend during 13 d to 19 d after fruit setting, and then increased significantly, showing that green turned to yellow. A total of 11 kinds of betalains were detected in Dahong, and the content of betanin was the highest. The total content increased gradually, and the increase was significant at 28 d. A total of 6 kinds of betalain components were detected in the Wucihuanglong, and leucine betaxanthin content was the highest, while the flesh only contained betanidin and tyrosine. There was no significant difference in the total content of betalains in flesh, but it increased gradually in peel and sepal. There was only one common component of betanidin between the two varieties. According to the correlation analysis, the a^* value of the three parts of Dahong was significantly positively correlated with the total content of betalains and extremely significantly positively correlated with the content of betanin. The b^* values in the peel and sepal of Wucihuanglong were significantly positively correlated with the total content of betalain and the content of leucine betaxanthin, while the correlation between the total content of betalain in the flesh and the a^*, b^* and L^* values was not significant. The principal component analysis of the betalains of the two varieties showed that Dahong extracted four principal components, and the cumulative variance contribution rate was 79.23%. The contribution rate of the first principal component was 34.30%, which mainly integrated the components of betanin and phyllocactin. The comprehensive contribution rate of the second principal component betaine and metabolites was 21.35%, mainly synthesizing 2,17-Decarboxyphyllocactin and betalamic acid. Two principal components were extracted from Wucihuanglong, and the accumulative rate reached 84.21%. The contribution rate of the first principal component betaxanthin was 61.71%, which mainly integrated leucine-betaxanthin, tyrosine-betaxanthin and other components, which provided a new idea for color evaluation and breeding of pitaya. In conclusion, the peel and sepal of Dahong and Wucihuanglong gradually changed color with the increase of betalains. The flesh of Wucihuanglong contained only metabolites of betalains, and did not change color. Combined with correlation and principal component analysis, it was further speculated that the red color of Dahong was mainly contributed by betanin, phyllocactin and 2,17-Decarboxyphyllocactin, and the yellow color of Wucihuanglong peel and sepal was mainly contributed by leucine-betaxanthin. This would provide a new idea for the evaluation of pitaya color. This study described the formation mechanism of color difference of pitaya, and would lay a theoretical foundation for exploring the color mechanism, color evaluation, as well as the development and utilization of betalains.