The invention discloses a flow cytometry electrofusion apparatus. The flow cytometry electrofusion apparatus comprises: a one-to-one cell fusion portion, a fusion cell detecting and sorting portion and a single cell collection portion. The one-to-one cell fusion portion is provided with a plurality of parallel cellular localization channels. Different cells can be adsorbed to ends of the channels, and two different cells can close to each other and be fused. The fused cells are placed until membranes of the different cells are completely fused, and then are put into the fusion cell detecting and sorting portion. The fusion cell detecting and sorting portion comprises a laser light source, a fluorescence detector and a deflector. The fused cells, i.e., red and green double fluorescent stained cells, are collected in a collecting tube. When collecting a fused cell, flow of droplet in the fluorescence detector is stopped. 200 [mu]l of cell culture medium is added to the collecting tube through a cell culture medium accumulator installed above the collecting tube to open the end of the collecting tube. The 200 [mu]l of the cell culture medium containing the fused cell flows into a well of a 96-well plate arranged blow the collecting tube. At this time, the flow of the liquid in a flow chamber is started, and the next fused cell is put into the next well of the 96-well plate. According to the present invention, one-time continuous accomplishment of one-to-one cell fusion can be realized, fusants can be detected correctly after fusing and each fusant can be cultured respectively.