This paper describes a novel cell fusion method which induces cell fusion between adhered cells through a microslit for preventing nuclear mixing. For this purpose, a microfluidic device which had 105 cell paring structures (CPSs) making cell pairs through microslits with 2.1 ± 0.3 μm width was fabricated. After trapping NIH3T3 cells with hydrodynamic forces at the CPSs, the cells were fused through the microslit by the Sendai virus envelope method. With following timelapse observation, we discovered that the spread cells were much less susceptible to nuclear migration passing through the microslit compared with round cells. This finding will provide an effective method for cell fusion without nuclear mixing, and will lead to an efficient method for reprogramming and transdifferentiation of target cells toward regenerative medicine.