To address the conflict between the limited payload capacity of a single launch vehicle and the substantial deployment demands of large-scale target payloads, this paper employs a two-phase manned lunar landing mission architecture, where on-orbit refueling connects Earth ascent and space transfer. Mission scale analysis and calculations were performed for manned lunar landing utilizing on-orbit refueling. Dynamic models for the four main phases—launch, rendezvous, Earth-Moon transfer, and lunar landing—were established, and overall mission design simulation analysis was completed. A mass estimation method was employed to compare the total mission mass and the scale of each stage between the traditional mode and the on-orbit refueling mode. In order to define phase-specific limitations and develop a mass model that takes into account in-orbit evaporation losses of cryogenic propellant, a mission model covering the four phases of launch, rendezvous and docking, Earth-Moon transfer, and lunar landing was built. Subsequently, mission windows were calculated, and full-process orbital simulations were conducted to analyze trajectory parameters and propellant consumption for each phase. Genetic algorithms were used to optimize parameters for the lunar landing phase. Mass estimation results show that, compared to the thousands of tonnes launch mass required by the traditional mode, the total launch mass for the on-orbit refueling scheme is below 500 tonnes, and the space transfer stage mass is on the order of tens of tonnes. The full-process simulation findings provide crucial references for engineering design, further elucidating the propellant consumption for each stage of the on-orbit refueling strategy.