The water jet trenching machines are generally employed to bury pipelines in the seabed with the purpose of protecting submerged pipelines from fishery activities, geological disasters, marine engineering operations, etc. In this work, the Arbitrary Lagrangian-Eulerian (ALE) method was adopted to carry out a three-dimensional numerical simulation of the water jet trenching process, and the effects of jet velocity, trenching velocity and seabed soil strength on jet trenching are studied, on this basis, the temporal and spatial evolution of the water jet flow pattern and seabed scour pit depth during the water jet trenching process are obtained. The results of the study show that the ditching depth increases linearly with the jet velocity in the initial stage, and the ditching depth is little affected by the jet nozzle moving speed. When the soil shear strength is greater than 50KPa, it is not suitable to work for the water jet trencher. It has certain reference value for the practice of submarine pipeline burying engineering, and expands the thinking for the in-depth study of water jet trenching technology.