High-performance 3D fabrics are widely used for ballistic protection. In this study, we conducted finite element analysis (FEA) to investigate the ballistic mechanisms of 3D layer-to-layer angle-interlock woven fabric (3DLAWF) and 3D through-the-thickness angle-interlock woven fabrics (3DTAWF) under impact. We constructed full-scale mesoscale fabric models for two 3D fabrics to examine the influence of 3D fabric structures on dynamic behavior and ballistic performance. Additionally, by comparing and analyzing the energy absorption patterns and failure mechanisms of the fabrics under ballistic penetration, optimization strategies for 3D fabric structures were proposed. This work reveals the impact damage evolution mechanisms, energy absorption mechanisms, and stress wave distribution patterns in these two fabrics, providing valuable guidance for the design of ballistic protection using 3D fabrics.