Background: Drought is a major limiting factor seriously influencing worldwide soybean production and its impact on yield, morphological and physiological traits depend on the timing it occurs and the intensity of water shortage. Only limited research has however been conducted on identifying the drought-tolerant genotypes at different growth stages (vegetative growth phase, reproductive growth phase and the whole growth phase) as well as evaluate the effectiveness and reliability of multiple phenotypic and yield-related characteristics in soybean. Results: Two pot experiments and a 2-year field experiment were conducted to evaluate soybean drought tolerance at different growth stages. The membership function value of drought tolerance (MFVD) was used to identify drought-resistant cultivars during vegetative growth phase and reproductive growth stage; the relative drought index (RDI) of yield was used to assess drought-resistant cultivars during the whole growing period. In this study, regression models built based on MFVD indicated that the variation of drought tolerant coefficient (DC) of R/ S, TRL, LAI and RSR could explain 73.70% of the total variation at vegetative growth phase. However, higher heritability only found in LAI and RSR, indicating the two traits could serve as reliable criteria for drought evaluation. Similarly, the DC of SPP, YPP, PH, PB, MSNN and STB could explain 94.30% of the total variation in MFVD according to stepwise multiple linear regression analyses at reproductive growth phase. Thus, these six traits were identified as indicators for screening drought resistance genotypes in soybean. In addition, correlation analysis revealed that the MFVD was significantly positively correlated with the DC RB , DC R/S , DC RSA , DC RSR and DC RBR at vegetative growth phase and DC YPP , DC SPP , DC RB, and DC PB at reproductive growth phase. This indicated that these traits were closely related to the drought resistance of plants.