The invention discloses a harvesting machinery cleaning system fan control method which includes the steps: 1) defining an inclined angle range alpha1-alpha2 as an ideal inclined angle range of a harvesting machinery cleaning system, defining time t as ideal tilted time of the harvesting machinery cleaning system, defining loss ratio w as ideal loss ratio of the harvesting machinery cleaning system, and defining rotating speed v as ideal rotating speed of a harvesting machinery cleaning system fan; 2) sensing an inclined angle alpha s, tilted time ts, loss ratio ws and current rotating speed vs of the fan; 3) comparing the inclined angle alpha s, the tilted time ts and the loss ratio ws sensed in the step 2) with the ideal inclined angle range alpha1-alpha2, the ideal tilted time t and the ideal loss ratio w, and judging whether the current rotating speed v needs to be changed or not; 4) adjusting the current rotating speed v until the sensed loss ratio ws returns into the range of the ideal loss ratio w when the current rotating speed v needs to be changed in the step 3). The invention further provides a controller and a control system.