Given the inherent susceptibility of laminated composites to delamination damage, numerous strategies have been introduced in recent years to enhance delamination resistance. One emerging approach is the use of 3D-printed interlayers; however, despite promising results in enhancing delamination resistance, the effect of interlayer cellular architecture on mode II interlaminar fracture toughness (ILFT) has not yet been investigated. Accordingly, this study designed an interlayer composed of PVA filament, with a thickness of 0.4 mm and a hexagonal cellular architecture. Also, to comparatively evaluate the effectiveness of the interlayer cellular architecture, the results were compared with those of the authors’ previous study, and the effect of replacing the square geometry with the hexagonal geometry was assessed while maintaining the materials and design parameters constant. The results demonstrated that the hexagonal interlayer increased the maximum load-bearing capacity by 25% and 34% compared with the control specimen and the square structure, respectively. Moreover, based on the compliance calibration method, the initiation and propagation values of ILFT (G_IIC^(ini.) and G_IIC^(prop.)) increased by 164% and 88%, respectively. Meanwhile, the G_IIC^(ini.) and G_IIC^(prop.) improved by 160% and 17%, respectively, compared with those of the square structure, indicating the superiority of the hexagonal geometry in controlling the propagation of delamination damage. Fractographic analysis further revealed that crack deflection and pinning, together with the deformation and breakage of the PVA filaments, altered the failure pattern and enhanced delamination resistance. Overall, the findings underscore the decisive role of the cellular architecture of 3D-printed interlayers in the interlaminar performance of composites.