Selecting high-yielding cultivars under drought is an important practice to improve crop production. Canopy temperature (T) shows a relative reliable association with grain yield. In this study, we compared the suitability of canopy T and other agronomic as well as physiological traits associated with grain yield under different water regimes. Field experiments over two seasons (2011–2012 and 2012–2013) were carried out under three water regimes, represented about 64, 76 and 89% of potential evapotranspiration, with 16 local winter wheat (Triticum aestivum L.) cultivars in each season. Results showed that cultivars with higher yield usually performed consistently lower canopy T under three water regimes, while the relationships of grain yield with other agronomic or physiological traits were more influenced by soil moisture. In addition, the relationship between canopy T and grain yield varied with different growth stages: From the time of heading to early grain filling stages, a more significant negative linear relationship (p < 0.001) existed under the three irrigation levels.