This paper proposes a dual-channel high sensitivity photonic crystal fiber sensor with rectangular air holes, which can detect the refractive index of a single sample or detect the refractive index of two samples simultaneously, to increase the detection efficiency and wavelength sensitivity of the sample refractive index. The sensor can reduce the times of filling, emptying and cleaning of the sample to be tested and save labor and time costs. The finite element method is used to thoroughly analyze the proposed structure’s sensing properties. The results show that when the sensor detects a single sample, the maximum wavelength sensitivity is 67,300[Formula: see text]nm/RIU, and the highest figure of merit (FOM) is 547 RIU[Formula: see text]. When the sensor detects two samples synchronously, the maximum wavelength sensitivity is 64,100[Formula: see text]nm/RIU, which is the highest level among the known sensors of the same kind. It has good application prospect in the field of high sensitivity refractive index detection.