The infection of Apple mosaic virus (ApMV) can severely damage the cellular structure of apple leaves, leading to a decrease in leaf chlorophyll content (LCC) and reduced fruit yield. In this study, we propose a novel method that utilizes hyperspectral imaging (HSI) technology to non-destructively monitor ApMV-infected apple leaves and predict LCC as a quantitative indicator of disease severity. LCC data were collected from 360 ApMV-infected leaves, and optimal wavelengths were selected using competitive adaptive reweighted sampling algorithms. A high-precision LCC inversion model was constructed based on Boosting and Stacking strategies, with a validation set Rv2 of 0.9644, outperforming traditional ensemble learning models. The model was used to invert the LCC distribution image and calculate the average and coefficient of variation (CV) of LCC for each leaf. Our findings indicate that the average and CV of LCC were highly correlated with disease severity, and their combination with sensitive wavelengths enabled the accurate identification of disease severity (validation set overall accuracy = 98.89%). Our approach considers the role of plant chemical composition and provides a comprehensive evaluation of disease severity at the leaf scale. Overall, our study presents an effective way to monitor and evaluate the health status of apple leaves, offering a quantifiable index of disease severity that can aid in disease prevention and control.