Loading individual oocytes is a critical step for injecting RNA, expressing heterologous proteins, performing electrophysiological measurements, and so on. However, existing methods remain a challenge for automatically loading multiple single oocytes into different locations. Herein, a novel microfluidic chip on a robotic manipulator (chip‐on‐robot) with feedback control for flexible manipulation of multiple oocytes within a large spatial range is proposed. The manipulator automatically controls the microfluidic chip to reach different locations based on imaging feedback. The microfluidic chip then utilizes the hydrodynamic focusing effect of the main channel to separate oocytes for individual loading or reloading under capacitive sensor feedback. The separation distance reaches approximately 16 times the oocyte diameter. Moreover, capacitive signal feedback on the number of oocytes for flow direction control ensures the separation of all oocytes. For close‐loop control of the loading/reloading process, image‐based oocyte detection is combined using deep learning to calculate the target position of the oocyte. Finally, an automatic sequence is achieved to load multiple single oocytes into a well chip by using the chip‐on‐robot. As a demonstration, the oocytes are reloaded into a specified location based on the conditions. The proposed chip‐on‐robot with feedback control has significant advantages in the micromanipulation of oocytes.