The invention discloses an intelligent method and a system for controlling alternate irrigation of local root zone of crops. The system comprises a signal collecting module and a control module, wherein the signal collecting module is used for collecting the soil water-content information of different root zones of the crops in real time and the control module is used for controlling the motor of the irrigation system by utilizing the water difference alternate threshold, upper limit and lower limit of the soil water content and practically measured soil water-content real-time information of all side root zones. The system is applicable to the automatic control on the alternate irrigation of local root zones of field furrow irrigation crops such as corns, cottons, potatoes and the like, fruit trees and greenhouse vegetable crops, has the advantages of land saving, water saving and energy saving, has low cost and simple operation and is convenient for being generalized and applied in large area.