Deficit irrigation is a common approach in water-scarce regions to balance productivity and water use, whereas drought stress still occurs to various extents, leading to reduced physiological performance and a decrease in yield. Therefore, seeking a rapid and reliable method to identify wheat varieties with drought resistance can help reduce yield loss under water deficit. In this study, we compared ten wheat varieties under three deficit irrigation systems (W0, no irrigation during the growing season; W1, irrigation at jointing; W2, irrigation at jointing and anthesis). UAV thermal imagery, plant physiological traits [leaf area index (LAI), SPAD, photosynthesis (Pn), transpiration (Tr), stomatal conductance (Cn)], biomass and yield were acquired at different growth stages. Wheat drought resistance performance was evaluated through using the canopy temperature extracted from UAV thermal imagery (CT-UAV), in combination with hierarchical cluster analysis (HCA). The CT-UAV of W0 and W1 treatments was significantly higher than in the W2 treatment, with the ranges of 24.8–33.3 °C, 24.3–31.6 °C, and 24.1–28.9 °C in W0, W1 and W2, respectively. We found negative correlations between CT-UAV and LAI, SPAD, Pn, Tr, Cn and biomass under the W0 (R2 = 0.41–0.79) and W1 treatments (R2 = 0.22–0.72), but little relevance for W2 treatment. Under the deficit irrigation treatments (W0 and W1), UAV thermal imagery was less effective before the grain-filling stage in evaluating drought resistance. This study demonstrates the potential of ensuring yield and saving irrigation water by identifying suitable wheat varieties for different water-scarce irrigation scenarios.