The article presents an answer to the current challenge about needs to form methodological approaches to the digital transformation of existing industrial enterprises (EIE). The paper develops a hypothesis that it is advisable to carry out the digital transformation of EIE based on considering it as a complex technical system using model-based system engineering (MBSE). The practical methodology based on MBSE for EIE digital representation creation are presented. It is demonstrated how different system models of EIE is created from a set of entities of the MBSE approach: requirements—unctions—components and corresponding matrices of interconnections. Also the principles and composition of tasks for system architectures creation of EIE digital representation are developed. The practical application of proposed methodology is illustrated by the example of an existing gas distribution station.