This paper presents a fully coupled three-dimensional solver for the analysis of interaction between pulsatile flow and large deformation structure. A partitioned time marching algorithm is employed for the solution of the time dependent coupled discretised problem, enabling the use of highly developed, robust and well-tested solvers for each field. Conservative transfer of information at the fluid-structure interface is combined with an effective multi-predict-correct iterative scheme to enable implicit coupling of the interacting fields at each time increment. The three-dimensional unsteady incompressible fluid is solved using a powerful implicit time stepping technique and an ALE formulation for moving boundaries with second-order time accurate is used. A full spectrum of total variational diminishing (TVD) schemes in unstructured grids is allowed implementation for the advection terms and finite element shape functions are used to evaluate the solution and its variation within mesh elements. A finite element dynamic analysis of the highly deformable structure is carried out with a numerical strategy combining the implicit Newmark time integration algorithm with a Newton-Raphson second-order optimisation method. The proposed model is used to predict the wave flow fields of a particular flow-induced vibrational phenomenon, and comparison of the numerical results with available experimental data validates the methodology and assesses its accuracy. Another test case about three-dimensional biomedical model with pulsatile inflow is presented to benchmark the algorithm and to demonstrate the potential applications of this method.