Abstract: Paper-based carbon fiber honeycombs exhibit advantages such as low density, high specific strength, and high specific stiffness. However, owing to the brittle nature of the cell-wall material, they are prone to local buckling and sudden failure under impact loading, which limits further improvement in their cushioning and energy-absorption performance. To address this issue, a shear thickening fluid-filled paper-based carbon fiber honeycomb (STF-CFH) composite structure is proposed in this study, in which a corn starch-based shear thickening fluid is introduced into the honeycomb cells. Drop-weight impact tests, high-speed photography, and coupled Eulerian–Lagrangian (CEL) finite element simulations were conducted to investigate the dynamic mechanical response, failure mode, and fluid–structure interaction enhancement mechanism of the composite structure. The results show that STF filling significantly improves the crushing stability of the paper-based carbon fiber honeycomb, transforming the failure mode from localized brittle failure to a more uniform global progressive crushing mode. Under an impact energy of 40 J, the mean crushing force and crushing force efficiency of the STF-CFH composite structure increase to 1.62 and 1.39 times those of the unfilled honeycomb, respectively. Under an impact energy of 80 J, the peak force decreases to 0.76 times that of the unfilled honeycomb, while the mean crushing force and crushing force efficiency increase to 1.81 and 2.38 times, respectively, demonstrating enhanced energy-absorption efficiency. Numerical results further indicate that, during impact, the STF inside the cells undergoes a sharp increase in viscosity under high shear, suppressing local instability of the honeycomb walls through lateral constraint and pressure transmission, and thereby promoting the participation of more cells in deformation and energy dissipation. The findings provide guidance for the design of lightweight adaptive honeycomb structures for impact protection.