The comprehensive evaluation of drought resistance at the germination stage was conducted in winter wheat cultivars from Xinjiang, which provided the theoretical basis for the evaluation and selection of drought resistant wheat varieties during the germination period. In this study, two methods that possessed 20% PEG-6000 treatment and marker-assisted selection (MAS) with the functional markers TaNRX-a1 and TaNRX-b1 located on the 5BS chromosome, were used for adjusting drought resistance in 83 Xinjiang winter wheat cultivars at the germination stage. Seven indexes including germination rate, germinating energy, germination index, root number, root length, seedling height and coleoptile length were measured, and the results suggested that the seven indexes were decreased by 30.86%, 23.91%, 31.37%, 0.43%, 31.07%, 50.27% and 6.60%, respectively. The allele frequency of TaNRX-a and TaNRX-b in 83 winter wheat cultivars accounted for 83.1% and 16.9%, respectively. The TaNRX-a allele with high drought resistance during seed germination is predominant, while this allele was observed 93.8%, 82.1% and 79.5% of local varieties, introduced varieties and improved varieties, respectively. By applying the weighted membership function method together with MAS for TaNRX-a, the cultivars Chang dong 5, Hanyangmai, Kayimuhong, Nawatiran, and Gaojiasuo represented higher drought resistance. The correlation analysis showed, that both the root length and the coleoptile length were highly correlated with D value (0.557 and 0.516), and they could be served as a sign in selecting for drought resistance of wheat. Thus, taking use of phenotype datasets and molecular markers, this work suggested a way to effectively evaluate the drought resistance of wheat during germination stage.