The transition of the agro-industrial complex of the Far Eastern Federal District to innovative-oriented development objectively enforces the activation of innovative and investment processes, as well as ensuring effective management of innovative development as a single complex of interrelated economic processes. The specific territorial zoning of the region’s AIC requires differentiation of the innovative development strategies of its individual sectors in accordance with the certain conditions of their functioning. The research is based on the study and generalization of scientific approaches to the issues of innovative-oriented development of the AIC, taking into account various factors: territoriality, zonality, economic potential, etc. The article formulates a set of provisions underlying the development of the innovative-oriented development concept of the AIC of the region. There was determined the set of strategic goals of its innovative development regarding the specifics of the subjects. The purpose of research is to develop a conceptual approach to innovative-oriented development of AIC of the region, in appliance with its specifications.