Few works use the fully three-dimensional computational fluid dynamic method to simulate the flow fields around the marine pipes with large aspect ratios due to the huge computation cost. In the present work, an operator-splitting method is used to efficiently solve the three-dimensional Reynolds Average Navier–Stokes governing equations of the fluid flow around pipes by separating the problem as a combination of a two-dimensional problem in the horizontal plane and an one-dimensional problem in the vertical direction. A second order total variation diminishing finite volume method is used to solve the model. The precision of the present model is validated by comparing the present numerical results of two typical three-dimensional cases with the available experimental and numerical results. The simulation results with a commercial software are also included in the comparison and the present model shows a higher performance in terms of computational time.