The invention provides a cell electrofusion chip device based on a columnar microelectrode array, which consists of a columnar microelectrode array chip, a printed circuit board and a flow passage control module. The columnar microelectrode array chip consists of a quartz substrate layer, a metal lead layer, a polymer insulated layer and a columnar microelectrode layer sequentially from bottom totop, wherein the metal lead layers of the columnar microelectrode array chip is electrically connected with the periphery printed circuit board in a bonding way, leads outside electrical signals ontoa columnar microelectrode, and leads a gradient electric field with enough strength to be formed between adjacent columnar microelectrodes; and the flow passage control module covers the columnar microelectrode array chip. In the invention, by loading electrical signals on the columnar microelectrode, queue and fusion among cells are controlled; simultaneously, the superiority that the columnar microelectrode array benefits the flow of the cells in chamber-tracts is utilized for realizing continuous stream fusion of the cells; and with the combination of the design of the array columnar microelectrode, the continuous, high-efficient and high-throughput fusion of the cells in the device is realized.