A sensor system of a surface plasmon resonance (SPR) for analyzing a characteristic of a substance and the measuring method thereof are provided. The system includes an optical device for generating a first light beam and a second light beam in sequence; a sensor device for respectively generating a first plasmon wave and a second plasmon wave in response to an optical characteristic change of the first light beam and the second light beam with respective to the substance, in which a resonance is generated from the first plasmon wave and the second plasmon wave respectively generating a first reflective signal and a second reflective signal; and a measuring device for measuring spectra of the first reflective signal and the second reflective signal and obtaining the measured value which is substituted into an operational formula to calculate a reference value used for analyzing the characteristic of the substance.
