The early and accurate acquisition of crop yields is of great significance for maintaining food market stability and ensuring global food security. Unmanned aerial vehicle (UAV) remote sensing offers the possibility of predicting crop yields with its advantages of flexibility and high resolution. However, most of the existing remote sensing yield estimation studies focused solely on crops but did not fully consider the influence of soil on yield formation. As an integrated system, the status of crop and soil together determines the final yield. Compared to crop-only yield prediction, the approach that additionally considers soil background information will effectively improve the accuracy and reduce bias in the results. In this study, a novel method for segmenting crop and soil spectral images based on different vegetation coverage is first proposed, in which pixels of crop and soil can be accurately identified by determining the discriminant value Q. On the basis of extracting crop and soil waveband’s information by individual pixel, an innovative approach, projected non-negative matrix factorization based on good point set and matrix cross fusion (PNMF-MCF), was developed to effectively extract and fuse the yield-related features of crop and soil. The experimental results on winter wheat show that the proposed segmentation method can accurately distinguish crop and soil pixels under complex soil background of four different growth periods. Compared with the single reflectance of crop or soil and the simple combination of crop and soil reflectance, the fused yield features spectral matrix FP obtained with PNMF−MCF achieved the best performance in yield prediction at the flowering, flag leaf and pustulation stages, with R2 higher than 0.7 in these three stages. Especially at the flowering stage, the yield prediction model based on PNMF-MCF had the highest R2 with 0.8516 and the lowest RMSE with 0.0744 kg/m2. Correlation analysis with key biochemical parameters (nitrogen and carbon, pigments and biomass) of yield formation showed that the flowering stage was the most vigorous season for photosynthesis and the most critical stage for yield prediction. This study provides a new perspective and complete framework for high-precision crop yield forecasting using UAV remote sensing technology.
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