Digital government governance is a crucial aspect of the modernization of the national governance system and governance capacity in the digital age. The integration of government governance and digital technology has driven the digital government governance to evolve from a systematic approach to a complex one. As a complex adaptive system, digital government governance encounters complex issues such as the “ diversity” of governance subjects and objects, the “competitive collaboration” of governance subsystems, and the “iterative convergence” of the governance process. To address the increasingly complex problems in digital government governance, system theory, as a formal theory and an interdisciplinary theoretical method, provides new solutions for systematic and complex issues. From the perspective of system theory, this paper analyzes the transformation trend of digital government governance formed by its characteristics of integrity, relevance, openness, and self-organization, and proposes key strategies for systematically promoting digital government governance innovation in dimensions such as governance subjects, governance technologies, governance rules, and governance models.