Photonic crystal fiber (PCF) based surface plasmon resonance (SPR) sensors show great promise in different fields due to their flexibility, remote accessibility, and remarkable sensing capability. To improve the performance (e.g. sensitivity) of PCF-based SPR sensors, two strategies are generally employed: (i) use of new plasmonic materials, and (ii) engineering the air-hole geometry. In particular, air-holes geometry plays a crucial role in maintaining both core and surface plasmon polariton (SPP) modes in SPR sensors. This work aims at investigating the effect of air-holes geometry on the performance of PCF-based SPR sensors. Here, three PCF models namely A, B, and C have been built with different air-hole geometries, and their effect on refractive index (RI) sensitivity is explored systematically through design, numerical simulation, data acquisition, and interpretation. Performance parameters such as confinement loss (CL), sensitivity, and sensing range of analytes (i.e. RI) have also been evaluated. Model A and B exhibit same maximum wavelength sensitivity and resolution of 5000 nm/RIU and 2 × 10⁻⁵ RIU⁻¹ respectively, where model B's air holes are rotated 90° compared to model A. Otherwise, model C introduces a small air hole at the middle of PCF, where the maximum wavelength sensitivity and resolution are found to be 8000 nm/RIU and 1.25 × 10⁻⁵ RIU⁻¹, respectively. Moreover, model C exhibits CL much higher than model A and B. In addition, model C shows larger detection ranges of analyte's RI. This analysis would be helpful in designing highly sensitive PCF-based SPR sensors for detecting a wide range of analyte's RI.