Hybrid fiber-reinforced polymers (HFRP) are susceptible to hygrothermal aging, leading to significant changes in mechanical properties, but the underlying mechanisms remain unclear. Hence, the hygrothermal aging and penetration failure behaviors of carbon/Kevlar hybrid fiber composites are studied. Samples with three typical hybrid stacking sequences (C2K4C2, C4K4, C6K2) with different hybrid ratio, sensitive to hygrothermal environments, are fabricated using molding method. Samples undergo the artificial accelerated aging at 30 °C and 60 °C. By combining finite element analysis simulations and quasi-static penetration tests, the variation patterns of the penetration properties of laminate under different aging conditions are analyzed. Results indicate that the stacking sequence significantly affects the evolution of moisture absorption and penetration properties. A balancing mechanism between short-term penetration performance improvement and long-term aging stability decline is revealed based on the position of CF and KF layers. Within a certain period, the maximum load and energy absorption initially increase due to Kevlar and matrix plasticization induced by moisture absorption, then gradually decrease due aging. Finally, at the microscopic level, hydrogen bonds form between the polar groups of water molecules and resin molecular chains, thereby weakening intermolecular forces and enhancing the matrix’s ductility. Micro/macro failure analysis reveals the interfacial failure and fiber/matrix debonding, clarifying the hybridization mechanisms. This study provides theoretical insights into the penetration resistance design of HFRP under hygrothermal conditions.