A side-hole fiber microfluidic sensor based on dual long-period fiber grating(LPFG) is proposed in this paper. The side-hole fiber (SHF) has two air holes, which are natural microfluidic channels, and the microfluidic sensor can be temperature compensated. The dual LPFGs are written on the side-hole fiber by a CO2 laser, and their resonant wavelengths are 1 268.7 nm and 1 385.8 nm, respectively. The experimental results show that, when the sensor is placed in a glycerol aqueous solution with a refractive index of 1.335~1.395, the refractive index sensitivities of the two LPFG resonance peaks are -88.724 nm/RIU and -79.474 nm/RIU, respectively, and the temperature sensitivities are 52.0 pm/℃ and 55.7 pm/℃, respectively. The sensing matrix of the sensor can be derived by using the refractive index and temperature sensitivity. The proposed microfluidic sensor with temperature compensation has good linear responsivity and can realize the simultaneous measurement of refractive index and temperature, which has potential value in the fields of environmental monitoring and food safety.