The invention provides a network topology checking method and a system thereof. Based on the method and the system, the network connection condition of an information system can be effectively and quickly ascertained. Meanwhile, a real topological graph that is consistent with the operation condition of the system is automatically generated. Moreover, the illegal dial-up condition of the information system is effectively found out. Operation, maintenance and test staffs are facilitated to quickly locating a potential safety hazard of the system so as to ensure the security of the information system. The method comprises the steps of asset importation, equipment classification, configuration acquisition and automatic parsing, boundary definition, equipment viability scanning, equipment login verification, equipment external connection status test, information summarizing and report generation. The system comprises an asset importing and equipment classifying module, a configuration acquiring and automatic parsing module, a boundary defining module, an equipment viability scanning module, an equipment login verifying module, an equipment external connection status testing module, and an information summarizing and report generating module.