Further development of the clarification of the objectives of the construction and use of system mathematical models in the formation and implementation of programs of innovative development of regions was achieved: clarification of how the conceptual apparatus is used (conducting a study of the semantics of the concept of innovative development and its components); problem analysis of innovative development of regions (complex analysis of the institutional environment of functioning); conducting economic-mathematical system analysis (taking into account the relationship between subsystems from the point of view of integrity); system modeling (evaluation of goals and means - resources); assessment of risks and determination of measures for their elimination or smoothing (continuous control and analysis of implementation and, if necessary, taking appropriate measures); application of a system of criteria for evaluating the effectiveness of management of innovative development at both the macro and meso levels with the possibility of timely adaptation to the economic situation (development and use of an innovative lever in the form of resource multipliers and their evaluation, based on the systemic interaction of all resources). The analysis of approaches in the management of innovative development of the country and its regions, in the form in which they are used at present, allows us to conclude that they are insufficiently effective for the implementation of measures proposed by state programs. A fundamentally new approach and concept is needed for the processes of forming and implementing programs, as well as for the very development of strategic program documents, necessary changes in management, initially focused on performance, with the help of clearly, mathematically based, formulated tasks, goals and management criteria. The system of managing the innovative development of the region should ensure the formation of optimal programs of regional development, which will allow for their preliminary assessment, analysis, tracking of possible scenarios of development of events and trends during implementation, correction of previously formed programs, using the capabilities of modern technologies. The study of the peculiarities of the development of regions in terms of innovative activity requires, first of all, a systematic study of the semantics of the concept of innovative development and its components. system modeling of complex objects takes into account all existing direct, reverse, cross connections, while management is implemented using information and communication processes and connections of the circuit covering all other circuits. "Management of regional development, in particular, innovative development", implies the existence of management objects and subjects, the developed model also includes management of the formation of operating conditions. Until now, system modeling is widely used in solving management tasks as a methodological approach for formalizing management goals and criteria, researching the mechanisms of functioning of system objects.