As the key principle of precision farming, variation of actual crop evapotranspiration (ET) within the field serves as the basis for crop management. Although the estimation of evapotranspiration has achieved great progress through the combination of different remote sensing data and the FAO-56 crop coefficient (Kc) method, lack of the accurate crop water stress coefficient (Ks) at different space–time scales still hinder its operational application to farmer practices. This work aims to explore the potential of multispectral images taken from unmanned aerial vehicles (UAVs) for estimating the temporal and spatial variability of Ks under the water stress condition and mapping the variability of field maize ET combined with the FAO-56 Kc model. To search for an optimal estimation method, the performance of several models was compared including models based on Ks either derived from the crop water stress index (CWSI) or calculated by the canopy temperature ratio (Tc ratio), and combined with the basal crop coefficient (Kcb) based on the normalized difference vegetation index (NDVI). Compared with the Ks derived from the Tc ratio, the CWSI-based Ks responded well to water stress and had strong applicability and convenience. The results of the comparison show that ET derived from the Ks-CWSI had a higher correlation with the modified FAO-56 method, with an R2 = 0.81, root mean square error (RMSE) = 0.95 mm/d, and d = 0.94. In contrast, ET derived from the Ks-Tc ratio had a relatively lower correlation with an R2 = 0.68 and RMSE = 1.25 mm/d. To obtain the evapotranspiration status of the whole maize field and formulate reasonable irrigation schedules, the CWSI obtained by a handheld infrared thermometer was inverted by the renormalized difference vegetation index (RDVI) and the transformed chlorophyll absorption in reflectance index (TCARI). Then, the whole map of Ks can be derived from the VIs by the relationship between CWSI and Ks and can be taken as the basic input for ET estimation at the field scale. The final ET results based on multispectral UAV interpolation measurements can well reflect the crop ET status under different irrigation levels, and greatly help to improve irrigation scheduling through more precise management of deficit irrigation.