We present a molecular-level investigation of the epitaxial crystallization of β-nucleated isotactic polypropylene associated with the minor and local topographic modification at the interface, i.e., the inclusion of an ethylene comonomer. The experimental results show that the relative fraction of β-crystal (Kβ) decreases progressively with increasing the amount of ethylene comonomer, which originates from a simultaneous reduction in the β-nucleation ability of a β-nucleating agent (N,N′-dicyclohexylterephthalamide, DCHT) toward propylene–ethylene random copolymers (PERs) and the growth rate of the β-crystal relative to the α-crystal. With the aid of molecular mechanics simulation, we demonstrate that such a topographic modification weakens the intermolecular interactions at the nucleation and growth interfaces, thereby modifying the epitaxial nucleation of the β-crystal and the growth kinetics of β- and α-crystals. The study reveals that the polymorph selection of the PERs/DCHT system is not solely determined by the lattice match but also profoundly influenced by the topography characteristics dependence of molecular interaction at the crystalline interfaces. Our fundamental insight could have important implications in the control of the polymorphism of polymers through the careful design of the topography of the nucleation and growth interfaces.