In order to quantitatively analyze and identify the risk evolution on ship pilotage in the specific waters, it is necessary for simulation of the dynamic system to effectively carry out the ship in-and-out the harbor for the purpose of safety control. Firstly, the degree of risk on different pilotage tasks was established and ship transition equation between Fairway, berth or in the vicinity, anchorage or roadsteads was proposed through the harbor pilotage workflow analysis. Secondly, with Markov chain transition matrix, risk simulation model of pilotage dynamic system was constructed under a state of stochastic transition and trends of dynamic risk in different pilotage tasks were analyzed. Thirdly, with the help of data binding scenarios on harbor pilotage status, risk simulation of harbor pilotage dynamic systems was built. Furthermore, examples verification was carried out through harbor pilotage samples in eastern China. The illustrative example shows that the transition of pilotage state has the steady state of Markov characteristics, which keeps stable after fluctuations. The non-symmetric flow of ship in-and-out the harbor causes pilotage risk fluctuation with the time change. The overall situation risk of ship pilotage remains a steady value of 0.41 parts per thousand while the individual risk of ship pilotage remains a steady value of 0.67 parts per thousand. Dynamic system simulation model using the Markov Chain Monte Carlo algorithm is suitable for maritime traffic risk analysis, and turns out the basic characteristic for the evolution of risk on marine traffic safety control.