Fiber hybridization can effectively solve the localized brittle fracture problem of composite honeycomb, but the interaction between different fibers leads to a very complex failure mechanism. Hence, 3D-printed hybrid continuous fiber composite honeycombs with a combination of carbon and Kevlar fibers are designed to study the structural failure behaviors by the experiment and simulation method. The experimental samples, including Onyx, carbon, Kevlar, carbon/Kevlar, and Kevlar/carbon composites, are fabricated based on Markforged 3D printing technology, and the crushing tests are conducted to evaluate the failure behaviors. An equivalence finite element modeling method to replace the heterogeneous microstructure of hybrid composites is proposed to analyze the failure behaviors. Results indicate that carbon/Kevlar honeycomb exhibits the highest energy absorption and cost effectiveness, while CFRP honeycomb demonstrates the highest load-carrying capacity. It is found that carbon/Kevlar and Kevlar/carbon honeycombs have significant hybrid effects compared to single-fiber honeycombs, which also reveals the hybrid mechanisms between carbon and Kevlar fibers. Furthermore, the Onyx honeycomb, lacking long fibers, exhibits brittle collapse, whereas other honeycombs show ductile collapse due to the presence of Kevlar fibers. Combining the simulation studies, the damage evolution mechanisms of honeycombs, including fiber/matrix tension and compression, shear damage, interface damage, etc., are further revealed. This work provides valuable insights into the design and failure analysis of 3D-printed hybrid fiber composite honeycombs.