Marine biofouling has long been a problem in the worldwide shipping sector, and there are no ideal solutions to prevent it. Previous studies primarily focus on height of marine biofoulers sticked to ship wetted surfaces, with other factors, such as hardness, shape, density, etc., remaining less consideration. Our recent studies show that any single element is not likely to completely describe the compositions of ship total resistance. Here we develop a smart numerical method which can precisely capture the characteristics of each single component of marine biofoulers in generating additional resistance. In the early paper, the standard model was modified by only taking into account the rotating and swirling of fluids over wetted surfaces of ships as a result of marine biofouling. Nevertheless, the modified model is found possible to further develop by considering potential jetting and surging of fluids induced by the specific features of macro-biofoulers. The results obtained from the twice-modified model are allowed to compare with those yielded from the standard model, with an apparent improvement of the total resistance, more consistent with measured, demonstrating that the twice-modified model behaves in a more reasonable manner in modeling the biofouling-induced ship total resistance. Another important finding in this paper is that the ship block coefficient is found to be modified due to inhomogeneous distributions of biofouling, with less in the fore parts and more in the aft parts of ships, leading to a growth of the ship block coefficient, in turn, a modification of ships’ shape. The objective of this paper is to reveal the relationship between ship resistance and the characteristics of the marine biofoulers using the modified numerical model.