In this paper, the stability of direct current (DC) microgrids with a constant power load (CPL) and a non-ideal source is investigated. The CPL’s negative impedance will destabilize the system, and disturbances in the non-ideal source will degrade the load voltage quality. In this study, we aim to: (1) overcome the instability of the CPL; (2) mitigate disturbances from the non-ideal source; (3) prevent the discontinuous harmonic current of high-frequency switching regulator from interfering with the source. Then, a stabilization method based on active damping which can achieve the above three objectives simultaneously is proposed. To obtain the stability conditions, the small-signal model of the system near the high-voltage equilibrium is established. Then, stability conditions are derived by eigenvalue analysis, and the domain of attraction near equilibrium is also obtained using the quadratic Lyapunov function. For the second objective, the key is to choose the optimal parameters to achieve disturbance attenuation. For the third objective, the active damper can separate the source from the switching regulator, which can prevent the discontinuous harmonic current. Moreover, the proposed method can be extended to multiple cases, and simulation results verify the effectiveness of the proposed method.