The present invention discloses a method and a system for controlling thickness of a circuit board insulating layer, wherein the method comprises the following steps of: determining a plurality of positions where thickness of the insulating layer is needed to be measured within the area, except a circuit, on the circuit board; drilling holes on the determined positions; determining the thickness of the insulating layer at the position by measuring depth of the drilled hole; and adjusting the thickness of the insulating layer according to the determined thickness and the thickness required by the insulating layer. The method in the present invention selects a plurality of positions within the area, except the circuit, on the circuit board to drill holes, and then measures depth of the drilled hole so as to determine thickness of the insulating layer, so the thickness of the insulating layer on the whole circuit board can be accurately measured on the precondition that no destructive slicing is performed on the circuit board, and thickness of the circuit board insulating layer can be effectively controlled according to the measured thickness.