Cities are testing grounds where technology triggers social change, especially megacities. The digital transformation of megacities reflects both the polarizing effects of digital technologies and the characteristics of complex social systems, making it a topic of theoretical and practical significance. Based on long-term observations of Shanghai’s public data sharing and opening, as well as urban digital transformation, this paper draws on the theory of complex holism and follows the theoretical chain of “management-element complexity–system complexity–management complexity”. It constructs an analytical framework for digital transformation management in megacities from two perspectives: management-element complexity (value philosophy, organizational form, operating mechanism, and technological system) and system complexity (information completeness, connectivity, and adaptability). This framework helps explain the evolutionary patterns of digital transformation management in megacities and deepens the understanding of urban digital transformation management and the management challenges brought about by digital technologies. This paper makes the following contributions: It adjusts the theory of complex holism and extends it to the field of complex social systems; it explores the mechanisms through which digital technologies amplify complex systems—by enhancing system connectivity, diversifying adaptive components, and accelerating urban digital transformation. This paper also explores the mechanisms underlying “emergence” in the digital transformation of megacities and discusses their practical implications. The findings provide useful insights for digital transformation management in China’s megacities.