The invention discloses a vapor phase cleaning system and method of a propellant tank. The system is provided with a cleaning agent storage tank and a waste liquid treatment device. The waste liquid treatment device comprises an extraction device and a rectification device, wherein the extraction device and the rectification device are connected through a pipeline. The rectification device is connected with the cleaning agent storage tank through a pipeline; waste liquid is extracted through the extraction device and divided into a cleaning agent layer and a propellant layer, and the cleaning agent layer enters the rectification device to be purified and then enters the cleaning agent storage tank for recycling. The vapor phase cleaning system can be automatically controlled and is safe and reliable, the treating effects on the waste liquid and waste gas are good, a cleaning agent can be separated and recycled from the waste liquid and used repeatedly, the cost is saved, and the system is environmentally friendly and free of pollution.