Maize residue cover (MRC) is an important parameter to quantify the degree of crop residue cover in the field and its spatial distribution characteristics. It is also a key indicator of conservation tillage. Rapid and accurate estimation of maize residue cover (MRC) and spatial mapping are of great significance to increasing soil organic carbon, reducing wind and water erosion, and maintaining soil and water. Currently, the estimation of maize residue cover in large areas suffers from low modeling accuracy and poor working efficiency. Therefore, how to improve the accuracy and efficiency of maize residue cover estimation has become a research hotspot. In this study, adaptive threshold segmentation (Yen) and the CatBoost algorithm are integrated and fused to construct a residue coverage estimation method based on multispectral remote sensing images. The maize planting areas in and around Sihe Town in Jilin Province, China, were selected as typical experimental regions, and the unmanned aerial vehicle (UAV) was employed to capture maize residue cover images of sample plots within the area. The Yen algorithm was applied to calculate and analyze maize residue cover. The successive projections algorithm (SPA) was used to extract spectral feature indices from Sentinel-2A multispectral images. Subsequently, the CatBoost algorithm was used to construct a maize residue cover estimation model based on spectral feature indices, thereby plotting the spatial distribution map of maize residue cover in the experimental area. The results show that the image segmentation based on the Yen algorithm outperforms traditional segmentation methods, with the highest Dice coefficient reaching 81.71%, effectively improving the accuracy of maize residue cover recognition in sample plots. By combining the spectral index calculation with the SPA algorithm, the spectral features of the images are effectively extracted, and the spectral feature indices such as NDTI and STI are determined. These indices are significantly correlated with maize residue cover. The accuracy of the maize residue cover estimation model built using the CatBoost model surpasses that of traditional machine learning models, with a maximum determination coefficient (R²) of 0.83 in the validation set. The maize residue cover estimation model constructed based on the Yen and CatBoost algorithms effectively enhances the accuracy and reliability of estimating maize residue cover in large areas using multispectral imagery, providing accurate and reliable data support and services for precision agriculture and conservation tillage. Full article