In order to determine the main factors influencing soluble chemical transfer and corresponding techniques for reducing fertilizer loss caused by runoff in irrigated fields, a physically based two-layer model was developed with incomplete mixing theory. Different forms of incomplete mixing parameters were introduced in the model, which was successfully verified with previous published experimental data. According to comparison, the chemicals loss of fertilizer is very sensitive to the runoff-related parameter while it is not sensitive to the infiltration-related parameter. The calculated results show that the chemicals in infiltration water play an important role in the early time of rainfall even with saturated soil, and it is mainly in the runoff flow in the late rainfall. Therefore, prevention of shallow subsurface drainage in the early rainfall is an effective way to reduce fertilizer loss, and the coverage on soil surface is another effective way.