The invention provides a method and a system for controlling seating of a rotary drilling rig mast. The control system comprises an amplitude-variable oil cylinder, a balance valve, an amplitude-variable control valve, a controller, a flow limiting device, a first electromagnetic valve, a second electromagnetic valve, a first sensing device and a second sensing device, wherein the flow limiting device is connected to the side of an oil circuit between a rodless cavity of the amplitude-variable oil cylinder and the balance valve; the first electromagnetic valve is arranged on a pilot oil circuit of the amplitude-variable control valve; the second electromagnetic valve is arranged on an oil circuit from the flow limiting device to an oil tank; the controller controls the first electromagnetic valve to be switched off and the second electromagnetic valve to be switched on after the mast is descended to a pre-arranged position via signals of the first sensing device and the second sensing device, and enables hydraulic oil of a rod cavity to flow back to the oil tank through the flow limiting device, so as to realize self-seating of the mast, as a result, adverse effects on the amplitude-variable oil cylinder and a related mechanical structure caused by difficulty in accuracy control of shrinkage of the amplitude-variable oil cylinder are avoided, and the service life of the mechanical structure is prolonged.