Bougainvillea is an important woody ornamental plant in southern China. There are a large number of varieties, but the classification is relatively chaotic. This study took 133 Bougainvillea varieties introduced and preserved in Yunnan as the research object, and conducted frequency distribution statistical analysis, coefficient of variation calculation, and diversity index calculation for 10 quantitative characters and 41 discrete characters. Q-type clustering analysis was also conducted. The results showed that the 133 Bougainvillea varieties had rich diversity in many characters, and the coefficient of variation of quantitative characters ranged from 19.61%–32.59%, with an average of 26.64%. The coefficient of variation of the total flower stem length, calyx tube width, petiole length, and flower length was the highest, and the diversity index ranged from 1.69–2.09, with an average of 1.92. The diversity index of leaf length, bract width, leaf width, and bract length was the highest. The diversity index of discrete characters ranged from 0.17–2.19. There were 11 discrete characters with H′ values greater than 1, and the diversity index of bract color and calyx tube color was both greater than 2. The diversity was rich. Among the four species of Bougainvillea, the diversity index of Bougainvillea×buttiana was the highest, with the richest diversity, followed by B. peruviana, B. glabra, and B. spectabilis, whose diversity index was the lowest, with less diversity. However, each species has its own advantageous characters. Among the 51 characters, 22 characters showed significant difference among species, which were of great reference value for identifying and classifying the varieties of Bougainvillea. Based on the types of bracts, the number of spines, and the size of leaves, 133 B. varieties could be grouped into four categories: double spiny less, double spiny more, single spiny less leaflet, and single spiny large leaflet. The research results show that the phenotypic characters of the 133 B. varieties tested have high diversity, and the quantitative trait variation types are rich. This study could provide scientific basis for systematic evaluation of B. germplasm resources, variety classification, and germplasm innovation.