Hybrid fiber-reinforced polymer (HFRP) composites possess excellent overall performances, but premature delamination between xenogeneic fiber-layers weakens their mechanical properties. Thus, the flexural behaviors of carbon/Kevlar HFRP laminates, toughened by carbon nanotubes (CNT) only between xenogeneic fiber-layers, is studied to reveal the high-efficient improvement. Three stacking sequences (C4/K4, [C2/K2]s, and [C/K2/C]s) are designed, and samples are manufactured through hand lay-up and compression molding. CNT is applied with an areal density of 0–8 gsm to toughen the interfaces only between several xenogeneic fiber-layers in [C/K2/C]s. Three-point bending tests and microscopic characterizations are conducted to evaluate flexural properties and failure modes. Results show that the flexural properties of HFRP with xenogeneic interface toughening display an increasing-then-decreasing trend as the areal density of CNT increases. The flexural modulus, initial failure strength and ultimate strength can be improved by 26.06%, 13.84% and 18.73%, respectively. Importantly, it is found that CNT-toughening only between several xenogeneic fiber-layers is more efficient in reinforcing HFRP than the same fiber-layers. This is due to the fact that interface toughening between xenogeneic fiber-layers can effectively suppress the buckling failure of Kevlar fibers, which has a significant effect on improving flexural properties. Finally, the crack-bridging of xenogeneic fiber-layers and CNT-bridging of cross-layer are also revealed. This work provides some valuable references for the design and application of HFRP.