Based on the coupling between the D-shape fiber and the microtube resonator in the whispering gallery mode, combined with the microfluidics, a refractive index sensor is proposed in this paper, in which the coupling region is fully encapsulated. This sensor requires a very little liquid sample (about 5 nL), is not fragile, and has better resistance to environmental perturbation, portability and repeatability than the general fiber-microcavity-coupled sensor. By the numerical simulation, the resonance properties of the microfluidic microtube resonator are investigated, and the refractive index sensing performance is analyzed. The research results show that the thickness of the mircotube-wall and the liquid refractive index have a great influence on the sensor performance. The shift of the resonance wavelength has a good linear relationship with the liquid refractive index. Meanwhile, the refractive index sensitivity is high (510.5–852.7 nm/RIU), and the Q-factor reaches up to 5.53×10⁴, the detection limit can arrive at 2.11 × 10^–6.