The invention relates to a network topology structure recognition method and system. The method includes the steps that protocol data packets are sent to target devices through ports of a switch respectively, and feedback data packets returned by the target devices are captured through the ports respectively; the feedback data packets of the ports are analyzed respectively to acquire first network connection information corresponding to the ports from the feedback data packets; the network topology structure of the target devices connected with the corresponding ports is determined according to the type of the first network connection information corresponding to the ports respectively. By means of the network topology structure recognition method and system, the operation of automatically scanning a network and accurately recognizing two-layer network devices can be conducted to achieve the purpose of presenting a comprehensive and true network topology structure, and the network topology structure recognition efficiency is improved.