The invention relates to a method, device and system for inspecting a moving object based on cosmic rays, and belongs to the technical field of radiation imaging and safety inspection. The method comprises the steps: detecting whether the speed of an inspected moving object is within a preset range or not; recording the moving track of the moving object through monitoring equipment; obtaining the information of charged particles in the cosmic rays through a position sensitive detector, wherein the information comprises the track information of the charged particles; carrying out the positioning matching of the moving track and the track information, and determining the moving object; carrying out the track reconstruction of the charged particles according to the information of the charged particles; and recognizing the internal material of the moving object according to the track reconstruction. Through the cosmic rays, the method, device and system inspect a moving vehicle, and can detect nuclear materials, drug and explosive materials carried by the vehicle.