Multi-Soil-Layering (MSL) is a kind of natural ecological and low-cost polluted water treatment technology, which shows the potential of removing many pollutants in polluted water with its unique structural design and treatment mechanism. This paper will evaluate the effects of different structural forms and operating parameters on the performance of MSL system, and deeply discuss the structural design and parameter optimization of MSL system. By comparing the effect of pollutant removal under different structures, the optimal MSL system configuration is determined to provide scientific basis and technical support for the actual water treatment project.