Organophosphate insecticides with broad spectrum and high efficiency make a great difference to agricultural production. The correct utilization and residue of pesticides have always been important issues of concern, and residual pesticides can accumulate and pass through the environment and food cycle, resulting in safety and health hazards to humans and animals. In particular, current detection methods are often characterized by complex operations or low sensitivity. Fortunately, using monolayer graphene as the sensing interface, the designed graphene-based metamaterial biosensor working in the 0–1 THz frequency range can achieve highly sensitive detection characterized by spectral amplitude changes. Meanwhile, the proposed biosensor has the advantages of easy operation, low cost, and quick detection. Taking phosalone as an example, its molecules can move the Fermi level of graphene with π–π stacking, and the lowest concentration of detection in this experiment is 0.01 μg/mL. This metamaterial biosensor has great potential in detecting trace pesticides, and its application in food hygiene and medicine can provide better detection services.