The invention relates to a flow electroporation device. The flow electroporation device comprises a support frame and planar electrodes used for limiting a fluid flowing channel, wherein two planar electrodes are embedded into the support frame in parallel; each planar electrode comprises a device which is electrically connected with a high-voltage pulse power supply, so that fluid moving along the fluid flowing channel passes through a pulsed electric field; materials of the planar electrodes are selected from one or several of aluminum, stainless steel, gold, silver, titanium, platinum, iridium, niobium, ruthenium, rhodium, molybdenum, tungsten and conductive ceramics or conductive materials taking gold, silver, titanium, platinum, iridium, niobium, ruthenium, rhodium, molybdenum, tungsten and conductive ceramics as coating layers or plating layers. According to the flow electroporation device, the shape of an inlet and an outlet in the support frame structure can be optimized, so that a cell-bioactive substance suspension solution can uniformly enter into an electroporation chamber; meanwhile, cells subjected to electric shock treatment and other materials generated by electrotransfection can also be smoothly discharged out of the electroporation chamber. The flow electroporation device can be applied to treatment of ultra-large volume of cell liquid; the electrotransfectionefficiency can be obviously improved; meanwhile, the survival rate of the cells can be obviously increased.