We propose and demonstrate a dual-channel microfluidic sensor based on a side-hole fiber (SHF) with two long-period fiber grating (LPFG) structures. There are two air holes in the SHF, which are natural microfluidic channels. We fabricate two LPFGs (long-period gratings LPG-A and LPG-B) in the SHF with the resonance wavelengths of 1268.7 nm and 1385.8 nm, respectively. Results show that the refractive index sensitivities of LPG-A and LPG-B are ?76.0 nm/RIU and ?71.1 nm/RIU, respectively. One can measure the refractive index of liquid samples in two channels simultaneously. The proposed dual-channel microfluidic sensor has advantages of good linearity response, fluidic technology compatibility, and easy light input/output coupling and system integration, which helps the sensor to have a potential application in environmental detection and food safety detection.