Abstract: Three-dimensional orthogonal through-thickness interlock woven carbon fiber composites exhibit significantly enhanced delamination resistance due to their unique through-thickness reinforcement, which is critical for structural reliability and long service life. To reveal the mesoscale mechanisms governing their interlaminar shear performance, this paper systematically investigates stress transfer paths and damage evolution under interlaminar shear loading through short beam shear (SBS) tests, micro-CT damage observation, and mesoscale finite element modeling. The results indicate that under SBS loading, compressive damage first initiates in warp yarns on the compression surface; subsequently, transverse tensile damage occurs in weft yarns on the tension side. Interlaminar shear damage originates in shear stress concentration regions within warp yarns and propagates axially. Interfacial debonding initiates at yarn/matrix interfaces in high-shear regions but is constrained by Z-binder yarns, preventing penetrating delamination. Z-binder yarns bear axial tensile stress and provide through-thickness constraint, effectively inhibiting debonding propagation. The simulated load–displacement curves agree well with experimental results, with peak load error within a reasonable range. Moreover, predicted damage types, locations, and spatial morphologies align with CT observations, demonstrating that the mesoscale model accurately captures failure behavior under interlaminar shear loading. This study systematically elucidates, from a mesoscale perspective, the intrinsic mechanisms by which the orthogonal through-thickness interlock structure resists interlaminar shear failure, providing a theoretical basis for structural optimization and engineering application of 3D woven composites.