In order to examine the factors affecting the three-dimensional dynamic behavior of pile foundation while soil shows strong nonlinearity, numerical simulations of several soil-pile-structure models subjected to strong shaking were performed. The tests were conducted using the large-scale shaking table at the E-Defense to investigate the response and failure of a nearly full-scale pile-structure system under multi-dimensional loading. It is shown that the numerical analysis can reproduce the behavior of the piles and superstructure as well as those of soil with a reasonable degree of accuracy, suggesting its applicability to soil-pile-structure system subjected to strong 3-D shaking.