Video-based point cloud compression (V-PCC) utilizes high efficiency video coding (HEVC) to compress geometry and attribute videos generated from dynamic point cloud projection. However, the HEVC exhaustive coding unit (CU) size decision process is complex and hinders the real-time application of V-PCC. To reduce the coding complexity of V-PCC, this paper proposes a method that combined hand-crafted features and lightweight neural network to accurately predict the best CU partition in advance. First, we extract hand-crafted features, including direct features (DFs) and indirect feature (IF), as mixed features. DFs are simple and require no additional calculation, while IF is obtained indirectly by transforming the global and local distortions of the CU extracted before size decision determination. Second, we propose a lightweight fully connected network (LFCN) as the backbone network, two feature types are used as inputs to the LFCN to predict whether the CU should be split into sub-CUs, and the LFCN can be fully integrated into the encoder with only about 1.58KB of additional parameters. Experimental results show that the proposed method reduces coding complexity by an average of 51.2% while Luma’s BD-TotalRate only increases by 0.1% on average under the All Intra (AI) configuration.