The invention discloses a method for organically correlating primary and secondary system connection diagrams of an intelligent substation. The method comprises the following processes: establishing a primary system model of the substation; establishing a secondary system model of the substation; correlating the secondary system model with the primary system model; and displaying a main wiring diagram of the substation after the correlation. According to the method, the primary system model is correlated with the secondary system model by configuring measurement parameters and switch parameters through interval partitioning of a primary main wiring diagram drawing process and voltage level based interval partitioning of a secondary IED model, so that the range of correlating and matching selected IED devices is greatly reduced, the rate of correlating primary and secondary systems is greatly increased, and the correlation process is more efficient and simpler.