The crop water stress index (CWSI), based on canopy temperature (Tc), has been widely used in evaluating plant water status and planning irrigation scheduling, but whether CWSI can diagnose the stress status of crops and predict the physiological traits and growth under combined water and salt stress remains to be further studied. Here, a model of CWSI was established based on the continuous measurements of Tc for two maize genotypes (ZD958 and XY335) under two water and salt conditions, combined with growth stage-specific non-water-stressed baselines (NWSB). The relationships between physiology, growth, and yield of maize with CWSI were analyzed. There were significant differences in NWSB between the two maize genotypes at the same and different growth stages; thus, growth stage-specific NWSBs were used. The difference in NWSB was due to the difference and change in effective leaf width. CWSI was closely related to leaf water potential, stomatal conductance, and net photosynthetic rate under different water and salt stress, and also explained the variations in leaf area index, biomass, water use, and yield. Collectively, CWSI can be used as a proxy indicator of high-throughput phenotyping maize performance under combined water and salt stress, which will be valuable for predicting yield and improving water use efficiency.