Despite large amount of spending, the Healthcare System lags behind the quality improvements expected by users and policymakers. Several analysis and studies motivate the hard of innovation in Health Systems (HS), meant as the inefficacy of innovations to translate in service impacts and outcomes. This study argues that a theoretical and methodological gap hamper the development of effective knowledge regarding Heath System Innovation Management (HSIM). Namely, missing to recognize and properly model the Health as a complex and dynamics system, it is missed the study of the behaviour of HS in response to the introduction of an innovation. To place a step toward in the understanding of the dynamics of innovation in Health Systems, this paper aims to review and critically analyze theoretical and modelling issues of HS literature, in order to elaborate effective directions and methodological support for the advancement of research dealing with the management of innovation in HS. The purpose is to generate and support a directions and implications for scholarly research on the management of innovation in Health Systems. By combining a critical literature review and the application of the General Morphological Analysis the research comes to the identification of the key morphological elements of researches focusing on HS innovation management, and also to outline the taxonomy of a research model for exploring HS. Scholarly research on HS innovation should comply with HS research ‘morphology’ and ‘HS model’ requirements. About morphology, it is argued to be: wide in perspective, at system level, focusing on both components and relations, capturing the dynamics, aimed to study, using soft models, and leveraging on simulations. About the model system that should support scholarly research on HS innovations, it is made of determinants, boundary, components and relations. This paper paves the way to bridge a gap in Health System management literature, by clarifying the methodological elements of a research. This limits the building of managerial theories and makes the health innovation management largely ineffective.