The integration of remote sensing technology and machine learning algorithms represents a new research direction for the rapid and large-scale detection of water stress in modern agricultural crops. However, in solving practical agricultural problems, single machine learning algorithms cannot fully explore the potential information within the data, lacking stability and accuracy. Stacking ensemble learning (SEL) can combine the advantages of multiple single machine learning algorithms to construct more stable predictive models. In this study, threshold values of stomatal conductance (gs) under different soil water stress indices (SWSIs) were proposed to assist managers in irrigation scheduling. In the present study, six irrigation treatments were established for winter wheat to simulate various soil moisture supply conditions. During the critical growth stages, gs was measured and the SWSI was calculated. A spectral camera mounted on an unmanned aerial vehicle (UAV) captured reflectance images in five bands, from which vegetation indices and texture information were extracted. The results indicated that gs at different growth stages of winter wheat was sensitive to soil moisture supply conditions. The correlation between the gs value and SWSI value was high (R2 > 0.79). Therefore, the gs value threshold can reflect the current soil water stress level. Compared with individual machine learning models, the SEL model exhibited higher prediction accuracy, with R2 increasing by 6.67–17.14%. Using a reserved test set, the SEL model demonstrated excellent performance in various evaluation metrics across different growth stages (R2: 0.69–0.87, RMSE: 0.04–0.08 mol m−2 s−1; NRMSE: 12.3–23.6%, MAE: 0.03–0.06 mol m−2 s−1) and exhibited excellent stability and accuracy. This research can play a significant role in achieving large-scale monitoring of crop growth status through UAV, enabling the real-time capture of winter wheat water deficit changes, and providing technical support for precision irrigation.