The variation coefficient analysis, genetic diversity analysis, correlation analysis, principal component analysis and cluster analysis of 647 island cotton germplasm resources were carried out in order to screen more diverse types of island cotton germplasm resources for parent selection and variety breeding in the future. The variation range of quantitative indexes of 647 sea island cotton germplasm resources was 2.46%~36.43%, indicating the rich diversity among sea island cotton germplasm resources. The number of stem hairs, leaf color, leaf hairs, petal basal spot size, main stem hardness, fruit branch type and style length of island cotton germplasm resources were variable, and these external descriptive traits could be directly used for the improvement of plant morphology. Genetic diversity analysis of quantitative indicators showed that the diversity of indicators reflecting fiber quality was more abundant than that reflecting yield, and germplasm resources could be used for improving fiber quality and maturity. Correlation analysis revealed a significant correlation between different quantitative traits. The complicated interaction mode implied a comprehensive evaluation by integrating multiple datasets in germplasm innovation. The principal component analysis showed that the cumulative contribution rate of the first five eigenvalues reached 75.76%. The first principal component was related to fiber quality, the second principal component was related to seed cotton yield, the third principal component was related to elongation, the fourth principal component was related to maturity, and the fifth principal component was related to lint percentage. When the genetic distance was 10, the germplasm resources were divided into 6 groups by cluster analysis. The comprehensive performance of cluster II was better. In actual breeding, targeted selection and improvement can be carried out according to breeding objectives.