The pendulum system with van der Pol type self-excitation is one typical self-excited mechanic system, and this paper studied the relaxation oscillation of the pendulum system. Firstly, the new time-scale and variable were introduced, so the pendulum system was described with standard slow-fast system. And then, on the basis of the geometric singular perturbation theory, the slow manifold and its structure of the system were obtained, and the relaxation oscillation was proved. Moreover, the expression of the relaxation oscillation and its period were obtained approximately. The analytical results indicate that, when the system undergoes relaxation oscillation, the pendulum passes through equilibrium position rapidly, and stays in the regions far away from the equilibrium position for a long time, and there are two break points which separate the fast dynamics from the slow dynamics. Numerical studies validate the analytical results.