A cell fusion device includes a chamber including a first input/output portion and a second input/output portion and providing a space through a fluid containing cells flows, at least one cell fusion structure provided in the chamber to form a fluidic channel through which the fluid flows and having a capturing portion adapted to capture the cell in the fluid and a fusion portion connected to the capturing portion and provide a space for fusing at least two cells trapped by the capturing portion and moved into the fusion portion in orders, a deformable membrane structure provided in the capturing portion of the cell fusion structure and configured to actuate to change a cross-sectional area of the fluidic channel of the capturing portion and to selectively capture the cell, and a membrane control portion configured to apply a pressure to the deformable membrane structure.