The invention discloses a non-oriented silicon steel operation control method and system. The non-oriented silicon steel operation control method comprises the following steps: recognizing the states of heating furnaces in a silicon steel hot rolling process; determining the current number of the heating furnaces according to the currently recognized states of the heating furnaces; invoking a first production data set to adjust the thermal expansion calculation coefficient and the cooling water quantity of each upstream frame for intermittent matching of current rolling when the determined number of the heating furnaces is three, wherein the first production data set corresponds to three-furnace production; invoking a second production data set to adjust the thermal expansion calculation coefficient and the cooling water quantity of each upstream frame for intermittent matching of current rolling when the determined number of the heating furnaces is two, wherein the second production data set corresponds to two-furnace production; and controlling the thermal expansion stable value of each upstream frame according to the adjusted thermal expansion calculation coefficient. Therefore, the leftwards turned E-shaped plate shape defect at the middle and later periods in the conventional rolling process can be overcome, and the plate shape defective rate in a downstream procedure can be reduced.