Canopy water interception is a key parameter to study the hydrological cycle, water utilization efficiency, and energy balance in terrestrial ecosystems. Especially in sprinkler-irrigated farmlands, the canopy interception further influences field energy distribution and microclimate, then plant transpiration and photosynthesis, and finally crop yield and water productivity. To reduce the field damage and increase measurement accuracy under traditional canopy water interception measurement, UAVs equipped with multispectral cameras were used to extract in situ crop canopy information. Based on the correlation coefficient (r), vegetative indices that are sensitive to canopy interception were screened out and then used to develop canopy interception models using linear regression (LR), random forest (RF), and back propagation neural network (BPNN) methods, and lastly these models were evaluated by root mean square error (RMSE) and mean relative error (MRE). Results show the canopy water interception is first closely related to relative normalized difference vegetation index (R△NDVI) with r of 0.76. The first seven indices with r from high to low are R△NDVI, reflectance values of the blue band (Blue), reflectance values of the near-infrared band (Nir), three-band gradient difference vegetation index (TGDVI), difference vegetation index (DVI), normalized difference red edge index (NDRE), and soil-adjusted vegetation index (SAVI) were chosen to develop canopy interception models. All the developed linear regression models based on three indices (R△NDVI, Blue, and NDRE), the RF model, and the BPNN model performed well in canopy water interception estimation (r: 0.53–0.76, RMSE: 0.18–0.27 mm, MRE: 21–27%) when the interception is less than 1.4 mm. The three methods underestimate the canopy interception by 18–32% when interception is higher than 1.4 mm, which could be due to the saturation of NDVI when leaf area index is higher than 4.0. Because linear regression is easy to perform, then the linear regression method with NDVI is recommended for canopy interception estimation of sprinkler-irrigated winter wheat. The proposed linear regression method and the R△NDVI index can further be used to estimate the canopy water interception of other plants as well as forest canopy.