This paper is concerned about the implicit-explicit (IMEX) methods for a class of dissipative wave systems with time-varying velocity feedbacks and nonlinear potential energies, equipped with different boundary conditions. Firstly, we approximate the problems by using the Hochbruck-Leibold IMEX method, which is a second-order scheme for the problems when the damping terms are time-independent. However, rigors analysis shows that the error rate declines from second to first order due to the nonautonomous dampings. To recover the convergence order, we propose a modified IMEX scheme and apply it to the nonautonomous wave equations with a kinetic boundary condition. Our numerical experiments demonstrate that the modified scheme can not only achieve second-order accuracy but also improve the computational efficiency.