Abstract: In the context of building digital China, it is particularly important to enhance digital governance capabilities to promote digital synergy innovation. Based on the Chinese regional governance framework, this study takes 278 cities in China as cases to explore the linkage effect and path selection of digital governance elements on the digital synergy innovation at different time periods. The results show that: (1) Digital synergy innovation can be divided into an embryonic period and a rapid development period, with a hierarchical effect in space. The eastern region has obvious advantages, while the central and western regions are accelerating their rise. (2) There are six high digital synergy innovation paths in the embryonic stage, which can be classified as digital government-environmental type and digital government-industrial type. There are five paths in the rapid development period, which can be classified as digital government-environmental type, digital industry-social type, and multi-dimensional synergy type. (3) Considering the evolution trend, in terms of single factors, digital infrastructure and innovation environment have always played an important role, and digital industry is prominent during the rapid development period; In terms of the relationship model, the digital government-environment type is relatively stable and gradually evolving towards a multi-dimensional synergy type. (4) Cross case comparisons find that there are differences in the improvement paths of digital synergy innovation in different regions. This study helps to grasp the digital synergy innovation current development, and provides important insights for exploring development paths at different time periods, improves the digital governance system, and accelerates the digital China construction.