The invention discloses a working method of an automatic cleaning type screw press. The method comprises the steps that 1, a containing cylinder is filled with fruit materials when it is guaranteed that a second valve is switched on, a first valve is switched off and a water inlet door is closed, a pressing plate moves downwards to press the fruit materials, and extracted fruit juice flows into a juice outlet pipe through a guiding through groove; 2, the pressing plate continues to move downwards, juicing is completed when the pressing plate makes contact with a lug on the water inlet door, then the second valve is switched off and the first valve is switched on, the pressing plate forces the water inlet door to overcome the acting force of an elastic part to rotate outwards to be opened, water in a water cavity of a second stand column flows into the containing cylinder through a water passing pipe and the water inlet door to flush seeds and peels left in the containing cylinder, and seeds and peels flow into a water outlet pipe along with water to be discharged; 3, the pressing plate moves upwards after cleaning, the water inlet door is closed again, the second valve is switched on, the first valve is switched off, and after the pressing plate moves upwards to a set position, the containing cylinder is filled with fruit materials again.