Abstract: With the continuous development of water transportation economy,ship traffic flow continues to increase,the problem of receiving pollutants from ships is gradually increasing,in which water pollutants from sailing ships can not be effectively received and water pollutants received by the ship receiving the waste of resources,the relevant departments and enterprises can not be effective,real-time communication and water pollution caused by water pollution is more and more obvious,so the receiving ship operations and regulatory process research is important for water.Therefore,the study on the operation and supervision process of receiving ships has important value and significance for water environment protection.Taking the receiving operation of water pollution mobile receiving ship in Chongqing main port area as the research object,this paper carries out Petri modeling from the existing receiving ship operation process,and finds out the related problems on the basis of formalization and mathematical description of the operation process.Pipe software is selected for optimization simulation modeling,and it is concluded that the optimized receiving ship operation process has the characteristics of high efficiency and stability enhancement,so as to further reduce the impact of the ship on the water ecological environment.