The effect of groups in conjugated molecules on films’ interface morphology, electronic structure, and charge transport behavior is explored utilizing a series of crystalline organic heterostructures that are constructed by four rod-like molecules and vanadyl phthalocyanine (VOPc). The four rod-like molecules, which possess the same biphenyl endgroup but different central groups, present similar growth behavior along with different thin film structural parameters and electronic structures. The changes of the structure parameters result in diverse morphology of the VOPc/rod-like molecule heterostructure because of the different lattice mismatch. The electronic structure differences in rod-like molecules cause different interface electronic structure of the heterostructure. Under the conjunct effect of morphology and interface electronic structure, the transistors based on the crystalline heterostructures present diverse charge transport behavior and field-effect mobilities. These results provide a clue for the development of crystalline organic heterostructure engineering and tailoring overall organic device performance through molecular design in local inducing layer.