A kind of dual micro-holes-based in-fiber Fabry-Perot interferometer sensor is proposed in this paper. The theoretical model of the reflection spectrum of proposed sensor is established based on the interference among four light beams, where both the relationships of the spectrum intensity with the length of micro-hole, refractive index (RI) of medium in cavity, transmission loss and reflection loss, and the characteristic parameters of fiber are demonstrated, and the temperature and RI responses of reflection spectra are also simulated. Through machining two micro-holes in single-mode fiber with 193 nm excimer laser, we fabricate the proposed fiber sensor which can be used for measuring the multi-physical quantities, and the corresponding experiments are demonstrated simultaneously. The results show that the sensor has better linear responses to temperature and RI change, and the corresponding linearity is superior to 99%. Due to having two sets of different temperature and RI sensitivities (i.e.-0.172 nm/℃ and 1050.700 nm/RIU; 0.004 nm/℃ and 48.775 nm/RIU) and better linearity, this kind of sensor can be used for measuring the temperature, the ambient RI and even the simultaneous discrimination of temperature and ambient RI. The RI and temperature resolutions are 1.010-5 RIU and 0.2℃, respectively. Furthermore, the sensor can also be used for sensing the gas pressure, and its measurement accuracy can reach to. 3 kPa. Owing to its high sensitivity, stability, small volume and easy fabrication, the sensor will be widely used in sensing technology.