Abstract: Three-dimensional (3D) woven composites, owing to their outstanding impact resistance and delamination tolerance, have been widely employed in the aerospace field. During the composite forming process, inevitable compaction deformation can significantly affect the final performance of the material. In this study, the compaction behavior of a carbon fiber twill layer-to-layer interlock woven preform was investigated through numerical simulation. A quasi-fiber-scale geometric model was established using a two-step modeling technique, and the compaction deformation process of the preform was simulated within an explicit dynamic framework. The reliability of the simulation results was verified by comparing them with Micro-CT observations of the preform microstructure under different compaction states. Based on the compaction simulation model, the relationship between macroscopic mechanical response and microscopic contact behavior was explored, and the evolution of yarn structure, fiber orientation angles, and fiber volume fraction distribution during compaction was analyzed. The results indicate that the virtual fiber model can accurately reproduce the variations in yarn path waviness and cross-sectional morphology during compaction. The contact and compression between fibers gradually evolve from the outer layers to the inner layers, and from inter-bundle to intra-bundle interactions. Moreover, both the fiber volume fraction at the warp–weft interlacing regions and the local fiber orientation angles on both sides of the interlacing points increase with applied pressure.