Pinus massoniana (Lamb.) is an important plantation species in southern China. Accurate measurement of P. massoniana seedling morphological indicators is crucial for accelerating seedling quality assessment. Machine vision, with its objectivity and stability, can replace human eyes in performing these measurements. In this paper, a measurement method for seedling morphological indicators based on Euclidean distance, Laplacian contraction, PointNet++, and 3D reconstruction is proposed. Firstly, multi-angle sequence images of 30 one-year-old P. massoniana seedlings were collected, distorted, and corrected to generate a sparse point cloud through the Structure-from-Motion (SFM) and dense point cloud through the Patch-Based Multiple View Stereo (PMVS). Secondly, a Dense Weighted Semantic Segmentation Model based on PointNet++ was designed, achieving effective segmentation of the P. massoniana seedling point clouds. Finally, a multi-iteration plane method based on Laplacian contraction was proposed. The new skeleton points were refined by minimizing the Euclidean distance, iteratively generating the optimal morphological skeleton, thus facilitating the extraction of morphological indicators. The experimental results demonstrated a good correlation between the machine vision-extracted morphological indicators (including plant height, ground diameter, and height-to-diameter ratio) and manually measured data. The improved PointNet++ model achieved an accuracy of 0.9448 on the training set. The accuracy and Mean Intersection over Union (MIoU) of the test set reached 0.9430 and 0.7872, respectively. These findings can provide reliable technical references for the accurate assessment of P. massoniana seedling quality and the promotion of digital forestry construction.