In this paper, a D-shaped photonic crystal fiber (PCF) sensor based on surface plasmon resonance has been presented. In the proposed structure, Graphene, Gold, and Silver have been used in different configurations in order to promote the sensitivity of the sensor. According to the numerical simulations performed by the finite element method (FEM) and considering the refractive index of the analyte from 1.36 to 1.40, the maximum wavelength sensitivity of 12600 nm/RIU has been obtained, which is related to the structure when the Gold layer sandwiched between two Graphene layers. This is while, the maximum amplitude sensitivity of the proposed sensor is 5708 (RIU-1), which is related to the configuration that Graphene has been placed under the Silver layer. On the other hand, the proposed structure is easy to use because there is no need to fill the fiber holes with the analyte and it can be easily placed on the D-shaped surface of the sensor. The proposed sensor is appropriate to sense the biological variation because of showing strong surface plasmon resonances. The effect of the fabrication tolerance on the proposed PCF is also studied. It is expected that the proposed model will be compatible with the bio-engineering approaches.