Traditional deep learning methods employing 2D images can only classify healthy and unhealthy seedlings; consequently, this study proposes a method by which to further classify healthy seedlings into primary seedlings and secondary seedlings and finally to differentiate three classes of seedling through a 3D point cloud for the detection of useful eggplant seedling transplants. Initially, RGB images of three types of substrate-cultivated eggplant seedlings (primary, secondary, and unhealthy) were collected, and healthy and unhealthy seedlings were classified using ResNet50, VGG16, and MobilNetV2. Subsequently, a 3D point cloud was generated for the three seedling types, and a series of filtering processes (fast Euclidean clustering, point cloud filtering, and voxel filtering) were employed to remove noise. Parameters (number of leaves, plant height, and stem diameter) extracted from the point cloud were found to be highly correlated with the manually measured values. The box plot shows that the primary and secondary seedlings were clearly differentiated for the extracted parameters. The point clouds of the three seedling types were ultimately classified directly using the 3D classification models PointNet++, dynamic graph convolutional neural network (DGCNN), and PointConv, in addition to the point cloud complementary operation for plants with missing leaves. The PointConv model demonstrated the best performance, with an average accuracy, precision, and recall of 95.83, 95.83, and 95.88%, respectively, and a model loss of 0.01. This method employs spatial feature information to analyse different seedling categories more effectively than two-dimensional (2D) image classification and three-dimensional (3D) feature extraction methods. However, there is a paucity of studies applying 3D classification methods to predict useful eggplant seedling transplants. Consequently, this method has the potential to identify different eggplant seedling types with high accuracy. Furthermore, it enables the quality inspection of seedlings during agricultural production.