To provide theoretical and practical guidance for rootstock breeding, 19 botanical traits of 70 eggplant germplasm resources for rootstock were investigated in this study, followed by the genetic diversity, principal component and cluster analysis. Moreover, tests for resistance to three soil-borne diseases (bacterial wilt, root-knot nematode and Verticillium wilt) were conducted. The coefficient of variation was variable from 15.9%-73.05% with an average of 46.11%. The genetic diversity index ranged from 0.325-2.008 with an average of 1.145. The coefficient of variation of weight per fruit was the highest (73.05%), and the genetic diversity of main stem diameter was the richest with an index of 2.0083. The component analysis revealed seven principal components (eigenvalues >1) with a cumulative rate of 76.55%. The 4th and 5th principal components were related to the convenience of grafting and the growth of grafted plant. The cluster analysis suggested three groups in this collection, including Group Ⅰ and Group Ⅲ were cultivated species, which showed no obvious differences in main stem color, leaf margin, fruit color and fruit size; Group Ⅱ contained four cultivated species and 20 wild germplasms, with the highest main stem diameter (20.42 mm) and the smallest fruit (the average length of 3.79 cm and diameter of 4.60 cm and weight of 73.38 g). 22 eggplant germplasms were detected with high resistance to bacterial wilt, 11 eggplant germplasms with high resistance to root-knot nematode and 7 eggplant germplasms with high resistance to Verticillium wilt. Three eggplant germplasms (BW9, LJ-7, Ng1-052) were highly resistant against bacterial wilt and root-knot nematode, and four eggplant germplasms (Ng1-003, Solanum khasianum C. B. Clarke, Solanum sisymbriifolium Lam., Solanum torvum Swartz) were highly resistant against root-knot nematode and Verticillium wilt. These eggplant germplasms can be used as resistance sources for disease resistance breeding. Based on the identification of botanical traits and disease resistance, three cultivars (LJ-18, Ng1-015 and Ng1-013) showing resistant against multiple diseases and vigorous growth and convenient graft were obtained, which laid a foundation for excellent multi-resistant eggplant rootstock breeding.