Health management system is a relatively new system formed in recent decades compare to other traditional systems in an aircraft. It comprises by on board part and off board part with a series of system contribute to the same health management function. Yet it expands rapidly with the evolution of enable technology. IVHM is an emerging concept which try to integrate the former separated health management related equipment and product. For such a new system in forming, it is a really good chance to apply system engineering method in defining the system functions, architecture and capture system requirements. With no previous endeavor put in this area, the system engineering could better illustrate the word integrate in IVHM concept. One step more, model based system engineering transforms system engineering as the world enter industrial 4.0 age. This paper introduces application of model based system engineering in designing health management system for civil aircraft. A functional analysis and requirement capture process is described in the paper using SysML diagram. Every use case for a function will be expanded into activity diagram/sequence diagram/state machine diagram to capture system functional and non-functional requirements. With this top down process the analysis can be independent from system already on board. This process helps keep traceability of requirements and better understand the working scenario of aircraft health management system. A health management system then modeled using this process. The modelling mainly helps system concept formulation and evaluation, system architecture design and requirements flowdown as well as clarify the future development of IVHM concept on civil aircraft.