A high quality factor Fabry-Pérot cavity (FPC) with smooth and flat micro-channel surface is realized by using a silicon on insulator substrate, in which the oxide layer functions as an etch-stop layer. And an optofluidic biosensor with integrated dual-channel Fabry-Pérot cavity is proposed for optical differential detection. A detection limit of 5.5×10^-8 refractive index unit is experimentally demonstrated, owning to the high quality factor of the cavity and the differential detection, which can extract the small signal for efficient amplification and greatly reduce the system noise.