In order to conduct surface modification more effectively, we have investigated the in-mold surface modification technique for composite surface that uses microstructures fabricated by imprint lithography. In the present study, we performed end notched flexure (ENF) tests to evaluate the resistance to crack propagation under macroscopic mode II loading at the modified carbon fiber reinforced plastic (CFRP)/adhesive interfaces by comparing the behaviors of brittle adhesives and ductile adhesives. In addition, we also investigated the influence of the aspect ratios (A) of the microstructures on the fracture toughness. From the ENF tests and microscopic observation of crack propagation, the mode II interfacial fracture toughness (GIIC) of the modified surfaces were found to be improved than that of flat surfaces regardless of applied adhesives. In the case of applying Epoxy A (3M DP-100 clear), which has a Young׳s modulus that is approximately 6.56 times higher and a mode I fracture toughness that is 1.34 times higher than Epoxy B (3M DP-105 clear), the cohesive failures of the CFRP concavo-convex microstructures occurred in addition to the microscopic interfacial failures during mode II loading. In addition, GIIC showed an almost constant value regardless of aspect ratio A. Thus, the interfacial fracture toughness of CFRP/Epoxy A was comparatively low compared to the CFRP cohesive failure, and the substantial crack length was almost constant, regardless of A, because the crack penetrated the concavo-convex microstructures. In the case of applying Epoxy B (3M DP-105 clear), the crack propagated along the CFRP/Epoxy B interface, including the plastic deformation of Epoxy B. Therefore, GIIC increased with an increase in A. Thus, we concluded that the substantially increased crack length was mainly influenced by the interfacial fracture toughness of CFRP/Epoxy A, which was comparatively higher than the cohesive failure of Epoxy B.