Fused deposition modeling (FDM) is a promising additive manufacturing technique for fabrication of continuous fiber-reinforced thermoplastic composites. For composite applications, the balance of material properties, including rigidity and toughness, needs to be considered. To overcome the drawbacks induced by single continuous fiber reinforcement, this study focused on the design and characterization of hybrid continuous fiber (continuous carbon and Kevlar fibers)-reinforced polyamide (PA)-based composites, prepared by 3D printing, to achieve comprehensive performance improvements and designable mechanical properties. The deformation and failure behaviors with the effects of hybrid conception, stacking sequences, and raster orientations of composites were investigated. A hybrid effect model was introduced to evaluate the hybrid effect of 3D printed continuous fiber-filled composites. Besides, compared to composites fabricated via conventional methods, a major difference in 3D printed hybrid composites is the performance of interfacial bonding. A roller peeling test was therefore conducted to investigate the interfacial strength of different materials. An analytical approach was developed to predict the tensile modulus of the printed hybrid composites by introducing an interfacial strengthening coefficient into the volume average stiffness model. The combined experimental and predicted results showed that hybrid composite specimens with separated distribution sequence showed a higher tensile modulus compared to hybrid composites with concentrated distribution. The higher tensile properties of the printed hybrid composites with separated continuous fiber-reinforced layers were attributed to the strong interfacial bonding, which delayed crack initiation and propagation.