In our previous paper (Bao et al., 2012 [1]), a general framework of using adaptive finite element methods to solve the Kohn-Sham equation has been presented. This work is concerned with solving the time-dependent Kohn-Sham equations. The numerical methods are studied in the time domain, which can be employed to explain both the linear and the nonlinear effects. A Crank-Nicolson scheme and linear finite element space are employed for the temporal and spatial discretizations, respectively. To resolve the trouble regions in the time-dependent simulations, a heuristic error indicator is introduced for the mesh adaptive methods. An algebraic multigrid solver is developed to efficiently solve the complex-valued system derived from the semi-implicit scheme. A mask function is employed to remove or reduce the boundary reflection of the wavefunction. The effectiveness of our method is verified by numerical simulations for both linear and nonlinear phenomena, in which the effectiveness of the mesh adaptive methods is clearly demonstrated.