Digital innovation activities are data-driven, and the process of organizational digital innovation is inevitably influenced by their key participants, employees, as well as changes in the social institutional environment. How government support and employee structure impact organisational digital innovation was examined in this study. Since digital innovation activities are data-driven, the mediating role of data flows within digital innovation ecosystems was explored. A quantitative research design was employed, and data were collected by a survey from 299 firms in China. Results of structural equation modelling using SPSS and AMOS reveal that government support for enterprises in terms of policies and services, as well as the employee structure within enterprises, have a direct impact on organisational digital innovation. Data flows within digital innovation ecosystems mediate the relationship between government support and organisational digital innovation activities. Our findings provided evidence for theories of digital innovation ecosystems and employee-driven digital innovation. The results and conclusions in this study can provide reference for enterprises to achieve digital innovation breakthroughs, and for policymakers to formulate digital-related policies and regulations.