A microfluidic cell-electrofusion device was developed for high fusion efficiency and automatic manipulation. It included an experimental platform, an electric signal generator and a microchip. Microstructure and controlling signal were elaborately chosen in order to realize precise cell manipulation, alignment and electrofusion. Compared with the traditional cell-electrofusion device, this device has some outstanding advantages. For example, short distance between two counter-microelectrodes will reduce the required voltage. A large number of microelectrodes can be fabricated on one small chip for high-throughput fusion. Transparent chip architecture benefited for microscopic observation and real-time recording. The integration of the experimental platform, signal generator and microchip is helpful for developing a portable cell-fusion system. On-chip electrofusion experiments of cucumber mesophyll protoplasts have been carried out and up to 40% fusion efficiency was obtained.