The invention provides a network topological graph automatic discovery method based on network probes under incomplete information. According to the method, under the condition of incomplete information, a network is divided into a plurality of zones effectively, affiliation relation between network equipment and each zone is provided, and connection relation between each probe and each zone is obtained, and thus network topology is discovered, and the method helps to realize further optimization of the network and improve safety performance of the network and the like. Compared with the existing method, the method only needs to obtain a certain amount of communication information, does not require communication between every two network equipment or special hardware support, does not need to send data packages actively to interfere the network, and can utilize the probes repeatedly to gradually refine the network structure, and has wide applicability.