To solve the problem of differences checking among the ICD/CID and IED of SCD in intelligent substation, a difference checking method as well as the tool is proposed. According to the grammatical features of SCD, ICD and CID, the stack technology is adopted to obtain the starting and ending line number of the nodes. As the complete units, the bilateral nodes join the cross checking on the tag name and key attributes to find the same nodes, and the differences of the non-key attributes, such as the out-of-order, different attribute values and contents. The starting and ending line of the same nodes on both sides can be displayed side by side. The details of differences in two kinds of files can be displayed intuitively and synchronously, as well as switched to original location of the document. The examples of typical substations illustrate the effectiveness of the proposed method. The tool can improve the accuracy and efficiency of difference checking among multiple documents. This work is supported by Science and Technology Project of State Grid Sichuan Electric Power Company (No. 52199717002A) and Science and Technology Project of State Grid Corporation of China (No. 521999160004).