This paper provides new insights into the impact resistance of 3D woven composites from a weft yarn distribution perspective. Two 3D through-thickness angle interlock (3D ATT) woven composites with aligned and misaligned weft yarn distributions were prepared for investigation. And a macro-meso combination model based on a bottom-up multi-scale framework was constructed to elucidate the damage evolution and dynamic response mechanisms of the composites during impact. The results show that the misaligned structure has superior impact resistance, more dispersed damage distribution, and less permanent damage at similar area density. The synergistic effect of finely dispersed resin pockets and misaligned yarns helped to retard the damage evolution, thereby improving the performance. The multi-scale simulation framework proved to be an effective tool for analyzing the mechanical properties of 3D woven composites, with misaligned weft yarns playing a critical role in stress and damage distribution. This research will aid in the design and application of 3D woven composites in impact resistant fields such as bird impact, ballistic impact, and explosions.