The digital innovation ecosystem is an important driving force for building a modern economic development system. It is of great significance to explore the multiple configuration paths of digital innovation ecosystems affecting the development of the low-carbon transformation of the economy to facilitate the green and sustainable development of the economy. We have found through our research that the types of configuration that lead to the development of a high-level low-carbon economy are ‘subjects-resource-environment linkage’ and ‘subjects-environment driven’. The former is the key configuration path that leads to the development of a high-level low-carbon economy. In both models, a high-level digital environment is the core condition that facilitates the development of a high-level low-carbon economic transformation. Moreover, in the spatial dimension, there is a significant difference in the types of configuration that achieve low-carbon economic transformation in the eastern, central, and western regions of China. The findings of this study reveal how the three major subsystems of the digital innovation ecosystem synergistically affect the low-carbon transformation of the economy. It not only helps to improve the relevant theories, but also brings certain references for improving the ‘synergy’ between low-carbon development and economic growth.