The traditional fault diagnosis method is generally based on the measuring signal, without considering the actual physical connection characteristics, but these characteristics affect the diagnosis results. With the wide application of professional electric system design software, system designers can easily obtain the physical connection characteristics and logical connection characteristics. By analyzing the signals of product layer or system layer, physical connection and its interconnected relationship, a set of logical physical synthetically (LPS) model, which unifies the abstract signal and the physical connection, was presented to study the LPS model instantiation method based on wire table and net table, and a set of intelligent fault detection software was developed. An example for validation was demonstrated: the fault diagnosis method based on LPS model can isolate the fault to the specified product level, with great value of engineering application.