Unstable characteristics of rootstocks can easily lead to quality degradation and yield declines for passion fruit. Therefore, this study focused on the seed characteristics, growth, chlorophyll fluorescence parameters under drought stress, and antioxidant enzyme activity of passion fruit rootstocks with three genotypes (R1, R2, and R3). A correlation analysis and a membership function method were adopted for a comprehensive evaluation, expecting to screen out passion fruit rootstocks adaptable to drought-prone areas in China. According to the study results, the three passion fruit rootstocks were evidently different in terms of the seed morphology and germination characteristics. Specifically, the seed width and 1000 seeds weight of R1 were significantly superior to those of R2 and R3, but the germination potential and germination rate of R3 were 87.9% and 93.3%, respectively, significantly higher than those of R1 and R2. Meanwhile, R3 exhibited a greater amount of aboveground biomass and a smaller root-shoot ratio, along with a more efficient water metabolic capacity. The chlorophyll fluorescence parameters, i.e., the initial fluorescence (F0), maximum fluorescence (Fm) and variable fluorescence (Fv), of the rootstock seedlings with three genotypes were not found to be significantly different under drought stress, while the Fv/Fm ratio of R2 was significantly higher than that of R1. The minimum values of H 2 O 2 and superoxide dismutase (SOD) appeared at 3 w after drought stress, and the minimum value of peroxidase (POD) and the peak value of catalase (CAT) were observed at week 4. As evidenced by the comprehensive evaluation, R3 is highly drought-resistant with good breeding potential.