Directly solving sophisticated partial differential equation constrained optimization problems is not only extremely time-consuming, but also very hard to find unique optimal solutions. Here, we propose stable and efficient surrogate models for seawater reverse osmosis desalination processes that enable thorough quantitative description of hydrodynamics and local transport characteristics in narrow flow channels. Without iteratively solving complex multi-physics simulation problem taking several hours, the proposed multi-scale design optimization framework significantly reduces the problem complexity by computing the surrogate models in seconds. Moreover, a fast-converging active subspace particle swarm optimization framework is proposed to address the optimal design problem. Compared to the standard particle swarm optimization algorithm, the proposed method enhances the average optimum by 14% and the standard deviation of optimum results for multiple runs is reduced by no less than ten times. The optimized desalination system achieves 9% reduction on energy consumption and 30% improvement on water production efficiency.