Electrofusion is an effective method for fusing two cells into a hybrid cell, and this method is widely used in immunomedicine, gene recombination, and other related fields. Although cell pairing and electrofusion techniques have been accomplished with microfluidic devices, the purification and isolation of fused cells remains limited due to expensive instruments and complex operations. In this study, through the optimization of microstructures and electrodes combined with buffer substitution, the entire cell electrofusion process, including cell capture, pairing, electrofusion, and precise separation of the targeted fused cells, is achieved on a single chip. The proposed microfluidic cell electrofusion achieves an efficiency of 80.2 ± 7.5%, and targeted cell separation could be conveniently performed through the strategic activation of individual microelectrodes via negative dielectrophoresis, which ensures accurate release of the fused cells with an efficiency of up to 91.1 ± 5.1%. Furthermore, the survival rates of the cells after electrofusion and release are as high as 94.7 ± 0.6% and 91.7 ± 1.2%, respectively. These results demonstrate that the in situ cell electrofusion and separation process did not affect the cell activity. This chip offers integrated multifunctional manipulation of cells in situ, and can be applied to multiple fields in the future, thus laying the foundation for the field of precise single-cell analysis.