When conducting nonlinear analysis of frame structure, we usually adopt plastic hinge model or plastic zone model which based on bending beam theory. But the effect of shear deformation on element deformation are not considered in the analysis model established based on bending beam theory, which is only applicable to the elements with large span depth ratio. For the main structure of steel mega-frame structures, the depth of element section is very high. Thus it can not meet bending beam theory assumption. The common analysis model can not simulate structure reaction accurately. This article puts forward some treatment methods for existing problems of nonlinear analysis of steel mega-frame structures, establish member element stiffness matrix based on improved finite segment element plastic zone model and consider the effect of element shear deformation on plastic development.