The objective of the physical topology discovery is to determine the connection relationship between various equipments in the network and the link between physical ports, which is very important for maintenance work, and with which the performance of the network can be monitored and evaluated efficiently and the fault discovery and positioning is also made easy. This paper proposes an optimization algorithm based on the predicate logic reasoning and the spanning tree protocol. It can effectively compute node information under the circumstances that the topology discovery AFT(Address Forwarding Table) data are incomplete. Thus the algorithm can overcome the shortcomings of the existing link layer network topology discovery, to obtain a possible physical topology network. This paper provides a new way to discovery link layer topology, with the link deducation technology, "to repair and revise" the uncomplete root AFT data. The shortcomings of the predicate logic and STP(Spanning Tree Protocol) algorithm are remedied, and the advantages are taken.