Genetic diversity analysis in crops plays an important role in evaluation and utilization of crop germplasm resources. In this study, the genetic diversity of 136 wheat (Triticum aestivum L.) germplasm resources with drought resistance were analyzed based on ten agronomic traits and their drought tolerance index (DTI) in rain fed (drought stress, DS) and well-watered (WW) environments. The results showed that length from flag leaf pulvinus to spike base (LFS) has the largest coefficient of variance (CV) of 42.1% and 37.2% in both DS and WW environments, respectively, while the spikelet per spike (SPS) has the smallest CV of 6.4% and 5.7%. Under different water regimes, spike number per plant (SNP), effective spikelet per spike (ESPS) and peduncle length (PLE) contribute a lot to the stable grain yield. Genetic diversity indices of DTI were from 1.95 to 2.07, with an average value of 2.02. Based on the DTI of agronomic traits, all accessions could be clustered into seven groups, the first and third groups are not sensitive to the water regimes, and the second group is more suitable for planting in dryland. The diversity message on the drought-tolerant plant material may be helpful for the DT improvement in wheat.