In this paper, a multi-body contact procedure for 3D explicit dynamic algorithm is constructed in the framework of S-FEMs. The multi-body contact is in the form of surface-to-surface contact and the contact algorithm uses the penalty function contact method. The dynamic behavior of cartilage and meniscus in the knee joint under linear loading and the dynamic behavior and the trauma level of the cranial structure during impact are analyzed. For the knee structure, a proper simulation is performed using the St. Venant's principle constitutive models, while the brain tissue has nonlinear and time-dependent properties and is simulated using a visco-hyperelastic constitutive model. Edge-based and face-based smoothed finite element methods (ES-FEM and FS-FEM) are used for contact simulations of the knee joint, while a combination of selective smooth finite element methods and the visco-hyperelastic constitutive model are used for dynamic simulations of contact for the unique properties of the brain. The numerical simulation results show that the S-FEMs has better accuracy compared to the conventional finite element method (FEM), and the selective smoothed finite element method has better ability to reduce element distortion effects and volumetric locking in soft tissues.