The solution exchange process is crucial in cell cryopreservation, an assistive reproductive technique that enhances reproductive autonomy and helps women overcome infertility challenges. Such a task is time-critical in the sense that the duration of cell exposure to the solutions significantly impacts cell viability. In this paper, a new micromanipulation system has been developed to automate such a task, where the contributions can be summarized as follows. This paper addresses the challenge of tracking cell positions within a microfluidic chip, due to the limitations of the microscope’s field of view (FOV). By utilizing a region control approach with visual feedback, the proposed method ensures that the cell remains centered in the image. Additionally, a real-time tracking method based on correlation filtering is presented, which precisely localizes cells and controls the syringe pump flow rate to mitigate delays and prevent cell loss. Experimental results illustrate the consistent positioning of the micro objects/cells at each step, the satisfactory success rate, and the robustness to the loss of vision feature. Integrated with novel manipulation strategies, our intelligent manipulation system offers a promising solution for in vitro fertilization (IVF), characterized by an embryologist-centered configuration and standardized robotic manipulation. This study aims to standardize clinical cryopreservation by transitioning from manual operation to a more efficient and reliable automated process. Furthermore, this approach can simplify procedures and enhance oocyte viability. Note to Practitioners—The motivation for this study was to propose an automatic method to address the challenges of manual cell cryopreservation, such as high operational complexity, low efficiency, and significant cell damage. Existing automated cell cryopreservation methods have shortcomings as they fail to simultaneously achieve comprehensive cell tracking and avoid damage caused by direct contact between cells and microtools. Additionally, the high complexity of robotic operations makes clinical application difficult. To overcome these limitations, this study introduces a novel robotic micromanipulation method based on microfluidic chip technology. This method enables full-process cell tracking, FOV tracking of the motorized stage, and non-contact manipulation during the exchange process of cells and solutions. Experimental results showed that the proposed method outperformed existing manual methods in terms of oocyte viability. For fertility experts and medical staff, such a robotic micromanipulation system can be combined with other automatic machines to provide a solution to cell surgery, achieving higher accuracy and efficiency.