The green ammonia synthesis process involves producing ammonia using hydrogen obtained from electrolyzing water with renewable energy sources, thereby contributing to carbon emission reduction and promoting sustainable development. However, in large-scale commercial operations, there exists a contradiction between the volatility of renewable energy and the stability required in chemical production processes: the fluctuation of the power supply and feedstocks constantly brings new changes to the heat and mass transfer of the fluid in the reactor, which will pose a severe challenge to the flexibility of reactor operation. In this study, we utilized a combination of reaction kinetics and computational fluid dynamics (CFD) to conduct three-dimensional modeling of the green ammonia reactor with validation against industrial data. The proposed novel approach facilitated the prediction of spatial flow field distribution within the reactor and assessment of varying load impacts on green ammonia yield and production index. The results indicate minimal deviation in processing parameters from baseline operating conditions under varying loads, yet a notable reduction in green ammonia yield occurs with decreased production loads, nearly reducing by 50%. Through the sensitivity analysis, the optimal operation scheme under different production loads is proposed. For example, at 30% load, the optimal operating pressure and hydrogen/nitrogen ratio are 14 MPa and 3.1, which are quite different from the baseline operating conditions. However, such process flexibility comes at the expense of catalyst and energy utilization, decreasing exergy efficiency by approximately 30% and potentially leading to operational anomalies such as gas dead spaces, low-temperature zones, and backflow, underscoring the trade-offs inherent in enhancing process flexibility. Nonetheless, the application potential of the green ammonia flexible synthesis process remains promising. Our proposed three-dimensional reactor simulation offers theoretical underpinnings for ensuring stability and optimal operation regulation in green ammonia production.