The refractive index sensing performance of the 8-fold quasi-periodic photonic crystal (QPhC) defect modes is studied. The proposed QPhC structure consists of the silicon columns immersed in a free-flowing liquid environment to enable real-time detection. The refractive index sensitivity of 982 nm/RIU, and a detection limit of 4.82×10−5 are achieved at the near-infrared wavelength. The influence of protein's thickness attached by the central dielectric column on the resonant wavelength is investigated. For the optimized radius of the central column r = 375 nm, the Q value of the resonant peak exceeds 4.9×104, and a slight variation of protein's thickness less than 1 nm attached by the micro-cavity can be distinguished. The spatial field distributions of the multiple defect modes and the corresponding sensitivity are analyzed and explained.