The panel zone, as an important part of the semi-rigid connection (SRC), can effectively affect the force transfer mechanism of the connection. This study aims to evaluate the panel zone mechanical characteristics through test on end-plate connection (EPC) and T-stub connection (TSC) under cyclic loading. Based on failure criteria, the mechanical properties of the panel zone are discussed, including the shear force, plastic energy dissipation, and failure modes. In light of the test studies, an effective and accurate numerical method in OpenSees platform for SRC with a behavior monitored by nonlinear rational springs is proposed. A 4 × 6 plane steel frame with SRC under the loading stimulation of 12 ground motions is conducted to testify the reliability of the model and analyze the panel zone behavior on the frame. The panel zones exhibit stable hysteresis characteristics and excellent ductility, and the analysis results of the effect of stiffness ratio between bolted connections and panel zone on frame energy consumption provide suggestions for structural energy dissipation design. The model conducts an accurate prediction of semi-rigid connection steel frames (SRCSFs) seismic behaviors considering the panel zone mechanical properties, and it can dramatically improve computing efficiency and is conducive to seismic design.