The logical circuits of smart substation secondary system follow IEC 61850 for modeling, while the design of physical circuits is still expressed with blueprint, which is unfavorable to the development of smart substation information technology. By referring to the modeling idea of logic circuits, a modeling method of the secondary system physical circuits is proposed. A model configuration process of physical circuits based on the concept of logical-physical decoupling is designed. The grammar and semantics of the physical circuit model are given. A complete engineering application solution based on the physical circuit model is realized, including the physical circuits configuration tool and physical circuits visualization tool. The key technology adopts the logical-physical corresponding in order to realize the association between physical circuits and logical circuits. The model configuration blank of secondary optical fiber and network structure is filled. It is convenient to import and export physical circuits configuration for the design tool and substation automation system. The application space of physical circuits model is extended.