The invention relates to a dual AD sampling inconsistency judging method for an intelligent substation. The method comprises the following steps that 1, dual AD sampling values of measured electrical quantity are acquired; 2, effective values and true effective values of fundamental waves of all cyclic waves of the dual AD sampling values of the measured electrical quantity are calculated separately; 3, whether the dual AD sampling values of the measured electrical quantity are valid or not is judged; 4, if yes, whether the dual AD sampling values are consistent or not is judged, wherein the judging method comprises the steps whether an absolute value of a difference value of the dual AD sampling values of the measured electrical quantity is larger than a preset threshold value or not is judged, and if yes, it is judged that the dual AD sampling values are inconsistent. According to the method, due to the fact that the validity of the AD sampling values of all ways is compared firstly, the possibility that misjudgment is caused due to the fact that in the judging process, the AD sampling values of all the ways are invalid, but the difference value of the dual AD sampling values meets the condition after being compared with the preset threshold value is avoided, and therefore, the judging accuracy is improved.