Estimating wheat yield is crucial for the quality of life and food security of a nation, particularly when crops face lodging stress, which severely hinders photosynthesis and maturation, resulting in yield loss. Rapid and accurate yield estimation is essential for disaster assessment and subsequent agricultural management. This study utilizes spectral, structural, and temperature data to comprehensively analyze the differential performance of multi-source data under two scenarios, selecting parameters that effectively represent yield differences under stress conditions. It also explores how the introduction of a specific parameter (the lodging index) affects the prediction accuracy of six wheat yield estimation models: eXtreme Gradient Boosting (XGBoost), Ridge Regression (RR), Random Forest Regression (RFR), K-Nearest Neighbors (KNN), Support Vector Regression (SVR), and Stacking Ensemble Learning (SEL). Compared with traditional models, the SEL model had the highest average prediction accuracy at 3 days after lodging (R²=0.64), 12 days after lodging (R²=0.70), and with combined multi-temporal features (R²=0.73). With the introduction of the lodging index, the prediction accuracy of all models improved to different degrees, and the SEL model showing an average R² increase of 8.19, 5.09, and 6.17%, respectively. Combined with the transfer learning methods such as transfer component analysis (TCA), joint distribution adaptation (JDA), and balanced distribution adaptation (BDA), the model maintained stable accuracy even with only 4% of the target dataset supplemented, achieving a high transfer prediction performance (R²=0.81). By optimizing the dataset under lodging stress scenarios and integrating ensemble learning and transfer learning techniques, the accuracy, stability, and transferability of wheat yield estimation models under lodging stress were effectively improved, providing a reference for wheat disaster assessment and the formulation of remedial measures.