In this study, we performed finite element method (FEM) simulations to optimize the configuration of gold nanorods (GNR) enhanced surface plasmon resonance (SPR) sensor and discovered its application for multiplex antigens detection. Our work analyzed the near-field coupling between the sensing film and GNR. By systematically study the effect of gold film thickness, GNR-to-film distance and GNR dimensions on SPR, it was found that for GNR width smaller than 40nm, length change in GNR brought about significant SPR wavelength shift on the sensor, while the sensor is insensitive for GNR-to-film distance. As an application, we adopted GNRs of width 20 nm and aspect ratios from 2 to 4 and demonstrated the concept of conjugating gold film and GNRs with anti-Immunoglobulin G (anti-IgG) antibodies for multiplex detection of various IgG proteins with more than 100nm separation on their SPR wavelengths.