In recent years, two-dimensional (2D) electronic spectroscopy experiments prove that the excitation energy transfer (EET) in photosynthetic light-harvesting systems presents long-lived electronic quantum beating signals. After being discovered in the light-harvesting system, the quantum coherence effect has aroused widespread discussion. To illustrate the EET process in the Fenna-Matthews-Olson (FMO) and phycocyanin 645 (PC645) complex, the local protein environment is often thought to be the same; however, this is ambivalent to the practical structural analysis of the light-harvesting complex. By adopting the dissipaton equation of motion theory, we present the effect of a heterogeneous protein environment on the energy transfer process with accurate numerical results. We demonstrate that the energy transfer process relies on the local heterogeneous environment for the FMO complex. A similar good agreement is found for the PC645 complex. Furthermore, we discuss the optimal value of different chromophores in the excitation energy transfer process by controlling the environmental characteristics.