Light plays a crucial role in the growth of fruit trees, influencing not only nutrient absorption but also fruit appearance. Therefore, understanding fruit tree canopy light transmittance is essential for agricultural and forestry practices. However, traditional measurement methods, such as using a canopy analyzer, are time-consuming, labor-intensive, and susceptible to external influences, lacking convenience and automation. To address this issue, we propose a novel method based on point clouds to estimate light transmittance, with the Leaf Area Index (LAI) serving as the central link. Focusing on apple trees, we utilized handheld LiDAR for three-dimensional scanning of the canopy, acquiring point cloud data. Determining the optimal voxel size at 0.015 m via standardized point cloud mean spacing, we applied the Voxel-based Canopy Profile method (VCP) to estimate LAI. Subsequently, we established a function model between LAI and canopy light transmittance using a deep neural network (DNN), achieving an overall correlation coefficient R2 of 0.94. This model was then employed to estimate canopy light transmittance in dwarfed and densely planted apple trees. This approach not only provides an evaluation standard for pruning effects in apple trees but also represents a critical step towards visualizing and intelligentizing light transmittance.