A biological sensing apparatus includes an optical waveguide substrate, a surface plasmon resonance (SPR) layer, and a lossy mode resonance (LMR) layer. The optical waveguide substrate includes a light input end and a light output end opposite to each other, and a biological sensing area is formed on one surface of the optical waveguide substrate between the light input end and the light output end. The SPR layer includes a metal layer and a plurality of biological probes. The metal layer is arranged on part of the biological sensing area, and the plurality of biological probes are evenly arranged on the metal layer. The LMR layer is arranged on part of the biological sensing area, and the LMR layer and the SPR layer are not overlapped. The present disclosure further includes a biological sensing system and a method of using the same.