In order to screen the drought resistance identification index and the drought-resistant alfalfa germplasm materials, and provide the theory and basic materials for the breeding of new drought-resistant varieties. In this study, we investigated the changes of root length, bud length, germination potential, germination rate, germination index, vitality index and root bud ratio of 59 alfalfa germplasms with different drought resistance that are from different region under drought stress condition, which was stimulated by using two treatments including distilled water and -0.6MPa PEG-6000 water solution. Correlation analysis, subordinate function coefficients, comprehensive drought resistance coefficient, grey relational analysis, stepwise regression and clustering analysis were used to evaluate the drought resistance and select evaluation indices in tested alfalfa cultivars during the germination period. The results showed that drought stress had significant effects on all indexes at the germination stage. By employment of this approach, we obtained three alfalfa genotypes, including Caoyuan NO.3, Sidey7 and WL903, which showed strong drought-resistant at the germination stage. These germplasms were selected as the research material for drought resistance breeding and drought resistance mechanism. Notably, root length, germination rate and vitality index were more sensitive than other indicators and could be used as a priority indicator for drought resistance identification and breeding of drought-resistant varieties. The results also showed that it is reasonable and accurate to use the comprehensive evaluation method with D value as the main index and WDC value as the auxiliary index in alfalfa to carry out comprehensive evaluation of drought resistance and screening of evaluation indicators.