A time domain finite element based method is employed to analyze wave radiation by multiple cylinders. The nonlinear free surface and body surface boundary conditions are satisfied based on the perturbation method up to the second order. The first- and second-order velocity potential problems at each time step are solved through a finite element method (FEM). The matrix equation of the FEM is solved through an iteration and the initial solution is obtained from the result at the previous time step. The three-dimensional (3D) mesh required is generated based on a two-dimensional (2D) hybrid mesh on a horizontal plane and its extension in the vertical direction. The hybrid mesh is generated by combining an unstructured grid away from cylinders and two structured grids near the cylinder and the artificial boundary, respectively. The fluid velocity on the free surface and the cylinder surface are calculated by using a differential method. Results for various configurations including two-cylinder and four-cylinder cases are provided to show the mutual influence due to cylinders on the first and second waves and forces.