Optical tweezers are widely used for noninvasive and precise micromanipulation of living cells to understand biological processes. By focusing laser beams on cells, direct cell manipulation with optical tweezers can achieve high precision and flexibility. However, direct exposure to the laser beam can lead to negative effects on the cells. These phenomena are also known as photobleaching and photodamage. In this study, we proposed a new indirect cell micromanipulation approach combined with a robot-aided holographic optical tweezer system and 3D nano-printed microtool. The microtool was designed with a V-shaped head and an optical handle part. The V-shaped head can push and trap different sizes of cells as the microtool moves forward by optical trapping of the handle part. In this way, cell exposure to the laser beam can be effectively reduced. The microtool was fabricated with a laser direct writing system by two-photon photopolymerization. A control strategy combined with an imaging processing algorithm was introduced for automated manipulation of the microtool and cells. Experiments were performed to verify the effectiveness of our approach. First, automated microtool transportation and rotation were demonstrated with high precision. Second, indirect optical transportations of cells, with and without an obstacle, were performed to demonstrate the effectiveness of the proposed approach. Third, experiments of fluorescent cell manipulation were performed to confirm that, indicated by the photobleaching effect, indirect manipulation with the microtool could induce less laser exposure compared with direct optical manipulation. The proposed method could be useful in complex biomedical applications where precise cell manipulation and less laser exposure are required.