The ease of controlling waveguide properties through unparalleled design flexibility has made the photonic crystal fiber (PCF) an attractive platform for plasmonic structures. In this work, a dual analyte channel’s highly sensitive PCF bio-sensor is proposed based on surface plasmon resonance (SPR). In the proposed design, surface plasmons (SPs) are excited in the inner flat portion of two rectangular analyte channels where gold (Au) strip is deposited. Thus, the surface roughness that might be generated during metal deposition on circular surface could be effectively reduced. Considering the refractive index (RI) change in the analyte channels, the proposed sensor is designed and fully characterized by the finite element method based COMSOL Multiphysics software. Improved sensing characteristics including wavelength sensitivity (WS) of 186,000 nm/RIU and amplitude sensitivity (AS) of 2,792.97 RIU−1 in the wide RI range of 1.30 to 1.43 is obtained. In addition, the proposed sensor exhibits excellent resolution of $5.38\times {10}^{-7}$ , signal to noise ration (SNR) of 13.44 dB, figure of merits (FOM) of 2188.23, detection limit (DL) of 101.05 nm, and detection accuracy (DA) of 0.0204 nm−1. Outcomes of the analysis indicate that the proposed sensor could be suited for accurate detection of organic chemicals, bio-molecules, and biological analytes.