The invention provides a cleaning method of a multistage variable-voltage pulse cleaning system. The cleaning method mainly comprises the following working procedures that firstly, liquid supplementing is carried out, wherein an object to be cleaned is placed in a cleaning cabin, a cleaning cabin cover is closed, and then a cleaning liquid is supplemented; secondly, heating is carried out, whereinwhen the cleaning liquid reaches a set liquid level, a heater is started to enable the temperature to rise to 45-55 DEG C; thirdly, vacuum pulse tank pumping is carried out, wherein a tank pumping valve is opened, a vacuum pump is started for pressure pumping, when high negative pressure is formed inside a vacuum tank, a gas-breaking valve is opened firstly, then a pulse valve is opened, the cleaning liquid is instantly poured into the vacuum tank, and forward pulse flushing is formed; fourthly, vacuum pulse pumping back is carried out, wherein the tank pumping valve, the gas-breaking valve and the pulse valve are closed, a vacuum-pumping valve is opened, the vacuum pump is started for pressure pumping, when high negative pressure is formed inside the cleaning cabin, a tank breaking valveand the pulse valve are opened, the cleaning liquid in the vacuum tank is instantly reversely flushed into the cleaning cabin, and reverse pulse flushing is formed. According to the cleaning method,labor is saved, the operation is simple and convenient, and the cleaning effect is good.