Optical tracking system (OTS) is widely used in robot orthopedic surgeries. During the surgery, the locomotion of the surgical instrument along different osteotomy planes and the adjustment of the patient’s body will lead to obvious variations on the spatial relationship among the positioning tools. Usually, the OTS is manually placed at a fixed viewpoint. As the size of the measurement volume (MV) of the OTS is limited, some positioning tools might move toward the boundaries of the MV, increasing the risk of navigation failure. This article proposes a two-phase optimization scheme for the active online adjusting of the OTS viewpoint to guarantee the consistency of navigation. A novel optimization structure is proposed with the consideration of continuous state inequality constraints. The dynamic accuracy of the OTS during the active adjusting is also demonstrated to be reliable. Ultimately, simulations and experiments are performed on an active navigation system (ANS) to verify the effectiveness of the proposed two-phase optimization scheme. Experimental results show that the OTS can be moved to the optimal viewpoint smoothly when confronted with significant variations on the spatial relationship among the positioning tools, guaranteeing the consistency of navigation. The navigation robot successfully keeps the positioning tools around the central region of the MV at different surgical phases.