A surface plasmon resonance sensing system and method thereof are disclosed. The system comprises an incident light source, a sensing element, a noble metal nanoparticle layer, a sample loading unit, and a light detector. The noble metal nanoparticle layer is composed of one of noble metal nanoballs, noble metal nanorods and noble metal nanoshells. The noble metal nanoparticle layer is disposed on the sensing element. The sample loading unit is used to allow a sample to be contacted with the noble metal nanoparticle layer. The light detector is used to detect an emergent light of the sensing element.