In this study, a nano-refractive index sensor is designed that consists of a metal–insulator–metal (MIM) waveguide with a stub-1 and an orthogon ring resonator (ORR) with a stub-2. The finite element method (FEM) was used to analyze the transmission characteristics of the system. We studied the cause and internal mechanism of Fano resonance, and optimized the transmission characteristics by changing various parameters of the structure. In our experimental data, the suitable sensitivity could reach 2260 nm/RIU with a figure of merit of 211.42. Furthermore, we studied the detection of the concentration of trace elements (such as Na+) of the structure in the human body, and its sensitivity reached 0.505 nm/mgdL−1. The structure may have other potential applications in sensors.