This article substantiates a scientific and methodological approach to designing the architecture of innovation development processes in the digital ecosystem of the region. The problem considered by the authors is solved by organizing and systematizing management processes at all levels of interaction. The paper presents the architecture of managing development processes and implementing innovations in the digital ecosystem of the region. It also provides a mathematical description of the levels and elements that form its target orientation. The aim of the work is to apply an architectural approach to the formation of target indicators for analyzing the innovative activity of interaction agents in the regional innovative environment as well as identifying signs and requirements for the structural description of the regional innovative environment as a milieu for the development of modern digital production technologies in basic areas in three organizational dimensions -“design”, “production”, “enterprise management”. As a result of the study, the authors identified 15 management systems that Russian enterprises need to implement for solving the challenges of innovation development at the level of regional, Russian and international superiority. The two-level architectural model proposed by the authors for designing a regional innovation environment as an ecosystem will be able to solve a set of management issues, to make informed management decisions on the development and implementation of investment programs and targeted development projects based on the collected, processed and extracted data.