The complicated biogeochemical behavior of matters in the water environment caused by sluice scheduling result in the transformation of water quality to present the characteristics of multi-media, multi-phase and multi-form. Based on the complex reaction mechanism induced by sluice scheduling in water environment system, a mathematical expression describing the mass transfer process of water components between various phases was proposed, a multi-phase transformation model of water quality with certain physical mechanism was established, and the water quality concentration under different sluice scheduling situations were simulated. By comparing with the no sluice scenario, the water quality concentration change rate under different sluice scheduling situations was calculated; the role of sluice scheduling in the transformation process of water quality was quantitatively evaluated; the driving effect of sluice scheduling on various reaction mechanisms in water was analyzed; and the dominant driving mechanism was identified. This study found that the change in pollutant concentration was significantly affected by sluice scheduling. Furthermore, the water quality concentration change rate was inversely associated with the change in the gate opening height, and the water quality concentration change rate in dissolved phase was larger than that in other phases. The strength and weakness of different dominant reaction mechanisms changed alternately with a change in sluice scheduling. For Huaidian Sluice, when the gate was fully open at 18 holes and the opening was approximately 40 cm, the contribution ratio of each corresponding reaction mechanism in water quality transformation was approximately same, and the dominance was relatively balanced, which could effectively suppress an increase in the nitrogen content and reduce the risk of nitrogen pollution.