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A novel photonic crystal fiber (PCF) sensor for refractive index detection based on polydimethylsiloxane (PDMS) is presented in this research, as well as designs for single-channel and dual-channel structures for this PDMS-PCF sensor. The proposed structures can be used to develop sensors with biocompatible polymers. The performance of the single-channel PDMS-PCF sensor was studied, and it was found that adjusting parameters such as pore diameter, lattice constant, distance between the D-shaped structure and the fiber core, and the radius of gold nanoparticles can optimize the sensor’s performance. The findings indicate that the detection range of the single-channel photonic crystal is 1.21–1.27. The maximum wavelength sensitivity is 10,000 nm/RIU with a resolution of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mn>1</mn><mo>×</mo><msup><mrow><mn>10</mn></mrow><mrow><mo>−</mo><mn>5</mn></mrow></msup></mrow></semantics></math></inline-formula> RIU, which is gained when the refractive index is set to 1.27. Based on the results of the single-channel PCF, a dual-channel PDMS-PCF sensor is designed. The refractive index detection range of the proposed sensor is 1.2–1.28. The proposed sensor has a maximum wavelength sensitivity of 13,000 nm/RIU and a maximum resolution of <inline-formula><math xmlns="http://www.w3.org/1998/Math/MathML" display="inline"><semantics><mrow><mn>7.69</mn><mo>×</mo><msup><mrow><mn>10</mn></mrow><mrow><mo>−</mo><mn>6</mn></mrow></msup></mrow></semantics></math></inline-formula> RIU at a refractive index of 1.28. The designed PDMS-PCF holds tremendous potential for applications in the analysis and detection of substances in the human body in the future.