The invention relates to a waveguide coupling metal photonic crystal biosensor and a detecting method thereof, which are used for the high-sensitivity sensation of biomolecule concentration and bioactive molecule idiosyncrasy. The waveguide coupling metal photonic crystal biosensor comprises a base, a waveguide layer and metal photonic crystals arranged on the waveguide layer. When the waveguide coupling metal photonic crystal biosensor is used for detecting, light transmitted by a light source irradiates the metal photonic crystals at an angle, and an optical detector is used for detecting an extinction spectrum of transmitted light passing through the waveguide layer and the base or detecting an extinction spectrum of transmitted light passing through the metal photonic crystals; after receptors are fixed on the metal photonic crystals, a sample solution flows through the surfaces of the metal photonic crystals, the detector is used for detecting the extinction spectrum of the transmitted light which passes through the waveguide layer and the base at the moment or detecting the extinction spectrum of the transmitted light which passes through the metal photonic crystals, and the two extinction spectrums are calculated by secondary extinction spectrums to quantificationally detect ligand concentration. The waveguide coupling metal photonic crystal biosensor has high sensitivity, low cost, simple preparation, simple use method, and the like.