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Large-scale forest inventory at the individual tree level is critical for natural resource management decision making. Terrestrial Laser Scanning (TLS) has been used for individual tree level inventory at plot scale However, due to the inflexibility of TLS and the complex scene of natural forests, it is still challenging to localize and measure every tree at large scale. In this paper, we present a framework to conduct large-scale natural forest inventory at the individual tree level by taking advantage of deep learning models and Mobile Laser Scanning (MLS) systems. First, a deep learning model, ForestSPG, was developed to perform large-scale semantic segmentation on MLS LiDAR data in natural forests. Then, the forest segmentation results were used for individual stem mapping. Finally, Diameter at Breast Height (DBH) was measured for each individual stem. Two natural forests mapped with backpack and Unmanned Aerial Vehicle (UAV) LiDAR systems were tested. The results showed that the proposed ForestSPG is able to segment large-scale forest LiDAR data into multiple ecologically meaningful classes. The proposed framework was able to localize and measure all 5838 stems at individual tree level in a 20 ha natural forest in less than 20 min using UAV LiDAR. DBH measurement results on trees’ DBH larger than 38.1 cm (15 in) showed that backpack LiDAR was able to achieve 1.82 cm of Root Mean Square Error (RMSE) and UAV LiDAR was able to achieve 3.13 cm of RMSE. The proposed framework can not only segment complex forest components with LiDAR data from different platforms but also demonstrate good performance on stem mapping and DBH measurement. Our research provides and automatic and scalable solution for large-scale natural forest inventory at individual tree level, which can be the basis for large-scale estimation of wood volume and biomass.