A temperature compensated fiber optic microfluidic sensor by using the femtosecond laser drilling technique is realized and studied. A laser-induced water breakdown method is used to fabricate a uniform microfluidic channel perpendicular with the fiber core, between a fiber Bragg grating (FBG) and the gold-coated end face of the fiber. Then a single end reflective sensor is made. By performing the fast Fourier transformation to the reflection spectrum of the fabricated device, both the FBG and Fabry-Perot (F-P) cavity wavelength information can be restored. Experiment shows that the FBG and F-P cavity can have different responses to the external temperature and the microfluidic refractive index. As a result, the temperature information can be sensed by measuring the FBG spectral shift, while the refractive index information can be extracted from the FBG spectral shift with the temperature compensated. In our experiment, the measured refractive index sensitivity of the sensor at a center wavelength of 1550 nm is about 1.2038 nm·RIU -1 (RIU is the unit refractive index). Analysis shows that the sensor performance can be further improved by optimizing the fiber structure. Our device is featured with structural simplification, easy operation, and real-time monitoring, and thus it can have good potential in both biochemical and medical areas.