A high-sensitive refractive index (RI) measuring method is proposed through the combined use of elliptical core photonic crystal fiber (PCF) and Sagnac interferometer. The sensing performance of the designed structure are studied theoretically using the finite element method. We analyze the phase birefringence and group birefringence to obtain the dependence of RI sensitivity on the operable wavelength λ. The RI sensitivity can be enhanced 10–20× by introducing a liquid-filled elliptical hole into the fiber core. Additionally, the single-core structure can convert to twin-core case just through decreasing the RI of filling liquid, and the spectral response is adjustable by changing main structural parameters. The simulation results show that the average sensitivity is about 1,14,967 nm/RIU within the RI range of 1.463–1.467, which corresponds to a resolution of 1.74 × 10−6 RIU. Finally, the sensing method is applied to magnetic-field measurement as an example, and the magnetic-field sensitivity can reach up to 3.45 $${\text{nm/Oe}}$$ within the range of 89.9–271.0 $${\text{Oe}}$$ . The measurement principle also applicable to other sensing fields, and the proposed structure is insensitive to fiber bending without fabrication complexity.