As a key node in port logistics systems, ship anchorage is often faced with congestion caused by ship flow fluctuations, multi-priority scheduling imbalances and the poor adaptability of scheduling models to complex environments. To solve the above problems, this paper constructs a ship scheduling algorithm based on a Markov-modulated fluid priority queue, which describes the stochastic evolution of the anchorage operation state via a continuous-time Markov chain and abstracts the arrival and service processes of ships into a continuous fluid input and output mechanism modulated by the state. The algorithm introduces a multi-priority service strategy to achieve the differentiated scheduling of different types of ships and improves the computational efficiency and scalability based on a matrix analysis method. Simulation results show that the proposed model reduces the average waiting time of ships by more than 90% compared with the M/G/1/1 and RL strategies and improves the utilization of anchorage resources by about 20% through dynamic service rate adjustment, showing significant advantages over traditional scheduling methods in multi-priority scenarios.