Robotic-assisted cell microinjection is widely used in biological areas. However, the large lateral vibrations of the pipette tip do great harm to cell membranes. In this paper, a spatial hub-type compliant mechanism (CM) applied in high-frequency penetration is proposed to reduce the vibration. By using the building blocks approach, the structure synthesis is done to design the hub-type CM. A static model is established by using the flexibility matrix method, and a dynamic model is established by using the lumped parameters method. Based on proposed design goals, parameter optimization of the CM is performed. The finite element simulations are conducted to verify the established analytical models. The results show that the RMS error of the static model and dynamic model is 0.73% and 6.1% respectively. To test the vibration rejection performance of the designed CM in a microinjection environment, an injection device equipped with the proposed hub-type CM is built and simulations are performed in comparison with a traditional injection device in the COMSOL software environment. Results show that the designed hub-type CM can well reduce the lateral vibration (i.e., 5.75 times in peak value).