Trajectory tracking technology has been the focus of industrial manipulatory applications for many years, and its research has been found in micromanipulation in bioengineering recently. In this paper, a hybrid vision and force control method is applied to the automatic cell injection. The three-dimensional cell injection process involves the trajectory tracking in free space and the force control in contact space. A PD plus feedforward compensation control method is applied to the trajectory tracking in 3D space. Further, a PD-based robust controller is introduced into trajectory tracking while the systemic uncertainty of the cell injection is additionally considered. Both of the two control methods are theoretically proved to be exponential convergent. Finally, the effectiveness of the proposed method is verified as compared with other control methods by its application to trajectory tracking problem.