One of the most popular applications of plasmonic photonic crystal fibers (PCFs) is refractive index (RI) sensing and biosensing. A novel surface plasmon resonance (SPR) microchannel PCF sensor with a D shape was developed. The PCF design was presented once with square and rectangular air holes and another time with circular and oval air holes for the comparison investigation to detect the analytes (decapeptyl, follitropin (FSH), and progsterone). The effect of the geometrical parameters of different air holes on the sensor’s optical properties has been numerically analyzed with a finite element method (FEM)-based COMSOL Multiphysics Program. Both proposed sensors offered confinement loss (CL) of 0.65 dB/cm and 0.55 dB/cm, interrogation amplitude sensitivity (AS) of − 437.15 RIU⁻¹ and − 340.96 RIU⁻¹, interrogation wavelength sensitivity of 5000, resolution of 8 $\times$ 10⁻⁵ RIU, and figure of merit (FOM) of 10.1 $\times$ 10⁴ RIU⁻¹. Changing the geometry of the air holes has an effect on the overall parameter behavior. The applied sensor can be suitable for the organic chemicals and biomolecule analyte detection.