This paper is the second part of the study on three-dimensional wave-pile group interaction analysis using the scaled boundary finite element method (SBFEM). The verified SBFEM model is employed to investigate wave interaction with pile group foundations. The leading pile experiences greater wave forces and larger displacement magnitudes than other piles. Parametric analyses in terms of wave properties and structural layouts are carried out. Compared with the pile distance, the wave number is a dominant factor affecting wave and structural behaviours. This study is expected to provide valuable information for the design of pile group foundations.