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• Determined the optimal UAV wide-band vegetation indices (VIs) for LAI and LCC retrievals. • Analyzed the sensitivity of VIs used for retrieval to influencing factors. • Constructed a hybrid inversion method of LAI and chlorophyll for individual apple tree crowns. • Quantitatively characterized the effect of canopy shading on inversion. The structural and chemical characteristics of individual apple tree crowns can indicate the nutritional and growth status of the trees, making them crucial for advancing orchard management practices. In this study, we collected multispectral imagery and ground validation data from two representative apple orchards in Beijing, China. We employed a hybrid inversion method to estimate the Leaf Area Index (LAI), Leaf Chlorophyll Content (LCC), and Canopy Chlorophyll Content (CCC) of individual apple tree crowns. Furthermore, we quantitatively evaluated the impact of canopy shading on the inversion results and mapped these traits at the scale of individual tree crowns (ITCs). To determine the optimal broad-band Vegetation Indices (VIs) for estimating LAI and LCC, we empirically analyzed 22 VIs using the PROSAIL simulation dataset. We constructed two measured datasets of canopy reflectance by masking canopy shadows, one containing shaded pixels and the other consisting of sunlit-only pixels. Using the Artificial Neural Network (ANN) algorithm and PROSAIL model, we developed a hybrid inversion model to assess the performance of the filtered VIs on the two measured datasets. The results demonstrated that TCARI/OSAVI and SR3 were the most accurate VIs for estimating LAI (including shaded pixels: R2 = 0.67, RMSE = 0.31 m2/m2; sunlit-only pixels: R2 = 0.74, RMSE = 0.28 m2/m2) and LCC (including shaded pixels: R2 = 0.70, RMSE = 7.11 μg/cm2; sunlit-only pixels: R2 = 0.73, RMSE = 6.63 μg/cm2) in the two measured reflectance datasets, respectively. Removing canopy shadows significantly improved the accuracy of LAI and LCC retrieval, although there was no significant difference in CCC retrieval accuracy (including shaded pixels: R2 = 0.78, RMSE = 31.25 μg/cm2; sunlit-only pixels: R2 = 0.79, RMSE = 28.48 μg/cm2). Moreover, we utilized UAV imaging multispectral data to map the estimated variability of leaf and canopy traits. The results revealed trait variability among different apple tree canopies, highlighting the potential of UAV imaging multispectral techniques in characterizing and mapping individual apple tree crown traits while capturing variability among crowns. We recommend performing canopy shading pixel masking to enhance the accuracy of ITCs trait retrieval. [ABSTRACT FROM AUTHOR]