To understand the genetic diversity among different green chrysanthemum varieties and provide theoretical support for the future breeding and improvement of green chrysanthemum varieties, this study conducted a genetic diversity research on 61 green chrysanthemum varieties through phenotypic traits and SSR molecular markers. The results showed that the 61 green chrysanthemum varieties had rich genetic variations both morphologically and at the molecular level. The coefficient of variation of 10 quantitative traits ranged from 12.01% to 168.34%, and the diversity index was between 1.35 and 2.05. The diversity index of 20 qualitative traits ranged from 0 to 1.40, with 16 phenotypic traits having a diversity index greater than 1, mainly concentrated on the morphology of the flower. Principal component analysis extracted 8 principal components, with a cumulative contribution rate of 75.138%. 20 principal component indicators such as leaf length, leaf width, and head diameter were selected as important bases for the morphological classification of green chrysanthemums. At an Euclidean distance of 20.0, the test materials could be divided into 3 major categories. 12 pairs of primers were selected from 89 pairs of primers, and a total of 59 clear bands were obtained, with 50 polymorphic bands, and the polymorphic band percentage was 84.75%. At a genetic distance of 0.4, all materials could be divided into 4 categories. A total of 61 chrysanthemum cultivars were completely discriminated using six out of twelve SSR primer pairs, and an SSR marker fingerprint of green chrysanthemum germplasm resources was subsequently constructed. The standards for morphological clustering and molecular clustering were more inclined to the presence or absence of secondary colors of ligulate florets, the type of capitulum, and the type of flower center. This study can provide theoretical references for the classification and identification, genetic variation, and variety breeding and improvement of green chrysanthemums.