To measure color phenotypic and pigment contents of chrysanthemum, we used 160 varieties of chrysanthemum as research materials. Pigment composition and contents were measured using UV spectrophotometry. Hyperspectral reflection values of different varieties and different parts of ray flowers and different flower rounds were measured by hyperspectral imaging technology. The relationship between hyperspectral reflection indices and pigment contents were analyzed using correlation analysis. The results showed that: 1) Data measured in the middle or rear part of ray flowers in the middle of wheels were stable. 2) Varieties of the same color had similar hyperspectral characteristics. Different varieties of chrysanthemum had significant differences in hyperspectral characteristics. 3) Hyperspectral reflection values RRed/RGreen, ARI, mARI, mCRI and TCARI showed a close correlation with pigment contents of ray flowers and their monitoring models were established accordingly using 80 varieties. 4) Using another 80 varieties as the verification materials, we found that models established with RRed/RGreen, ARI and mARI for anthocyanin content monitoring, and models established with mCRI for carotenoid content monitoring and models established with TCARI for chlorophyll monitoring had high accuracy. The established models can be used for nondestructive and fast determination of pigment composition and contents of chrysanthemum. Our research provides new ideas and methods for color phenotypic analysis and measurement of pigment composition and content of ornamental plants.