In order to understand the relationship and improve the use efficiency of Tagetes patula germplasm resources, analysis of genetic diversity and principal component of 40 Tagetes patula germplasms was carried out in terms of 18 traits. The results showed that the phenotypic diversity was abundant in Tagete spatula germplasms, and the higher variation of phenotypes was detected among accessions in phenotypic traits. The coefficient of variation ranged from 3.92% to 46.25%, with the largest for flower number followed by crown diameter and plant height. Shannon diversity indices indicated the higher diversity in frond (leaf) and flower traits with the average above 2.0. Moreover, the phenotypic diversity was more abundant in domestic germplasm than that in imported varieties. Four principal components with the variance cumulative contribution rate of 78.949% were obtained and 10 accessions with better comprehensive characters were screened out based on the principal component analysis. When the Euclidean distance was about 7.29, 40 accessions tested could be classified into two groups. The first group included 2 varieties (Shuixing yellow and orange) with the higher growth potential, and the second one containing 38 accessions that could be further divided into 2 sub-groups with flower color differences at the Euclidean distance about 6.0, suggesting that the growth potential and flower colour may be considered as the important indicators for classification of Tagetes patula germplasm based on phenotypic traits.