Low-frequency and large-amplitude vibration of flexible appendages in space can be induced when a spacecraft performs attitude maneuvers and thermal alternations during orbit operation. In this paper, a novel joint mechanism combined with a semi-active method for variable stiffness control is proposed to suppress the low-frequency vibrations of flexible jointed appendages. The variable stiffness of the joint is derived from the linear relationship between its output torque and rotation angle when direct current (DC) power is applied to the coils. Based on the Lagrange equation and the assumed mode method, the coupling dynamic relationships of the active joint and two flexible appendages are established, and semi-active vibration control simulations are performed. A ground experimental platform is built to simulate the microgravity environment in space. The frequency shift effect of rigid body motion and elastic vibration under impact disturbance are investigated. In addition, the effect of variable stiffness control on the elastic deformation of flexible appendages is studied. The simulation and experimental results indicated that the proposed method can control both the rigid body motion of the system and the elastic vibration of the appendages. It has been found that the major frequency bandwidth of the interference signal is within 0.3–1.0 Hz with a substantial vibration attenuation of 1.82–16.62 dB for the joint and 4.86–11.48 dB for the flexible appendages.