The Cu/zinc oxide (ZnO)/Al2O3 catalyst is highly favored in the hydrogenation of dimethyl maleate (HDMM) to coproduction of 1,4-butanediol (BDO), γ-butyrolactone (GBL), and tetrahydrofuran, and an in-depth study on its catalytic principle has a long-standing interest in the current study. Herein, by combining density functional theory and kinetic Monte Carlo simulations, we revealed the dominant pathways and reaction network of the HDMM process on the ZnO/Cu(111) surface. The effect of Cu–ZnO synergy is reflected in promoting the anchoring of ester carbonyls and decreasing the difficulty of hydroxyl group formation, which was clarified by mechanisms, density of states, and Bader charge analyses. From the perspective of constructive modification of active sites, a strategy was proposed to improve the GBL formation rate by decreasing the barrier of methanol removal based on the concepts of degree of rate control, and the BDO selectivity could be improved by increasing the barrier of the out-of-ring C–O bond cleavage in GBL hydrogenation. From the perspective of the external environment, the optimal reaction conditions of different target products were determined by manipulating the temperature and pressure. This study provides a guide for modifying active sites in Cu/ZnO/Al2O3 catalysts and potential possibilities for studying the complex reaction systems involving C4+ substances by multiscale simulation.