In order to define accurately the different flower phenotypes of lotus, a colorimeter was used to measure the various flower colors of 66 lotus cultivars. A numerical taxonomical study of flower colors was carried out by cluster analysis and ISCC-NBS method of designating colors. The results showed that the classification results obtained by cluster analysis could not fully represent the classification characteristics of lotus flowers; however, the ISCC-NBS method of designating colors was preferably corresponded with CIELab color system. According to the standard, all colors were divided into six groups (yellow, white, light pink, moderate pink, pink purple and red), and the numbers of white and moderate pink samples were more, accounting for 22.72% and 24.24% of the total number of samples. Each color group had correspondence with the L^*, a^*, b^* values of CIELab coordinate, so the quantitative description of the color of different lotus cultivars could be realized. What’s more, the flower colors of the lotus cultivars were various and the color differences of different color systems were significant. Although there was a negative correlation between the lightness value and chroma value of the lotus flower phenotype as a whole, it was clearly divided into two groups in the two-dimensional coordinates of the lightness value and chroma value. The first group contained yellow and white groups; and the second group contained light pink, moderate pink, pink purple and red groups. In conclusion, the combination of instrument color measurement and ISCC-NBS method of designating colors can more accurately define the classification of lotus flower color, which provides a theoretical basis for the identification of lotus cultivars and flower color breeding.