The increasingly complex national innovation system urgently needs modern scientific methods and tools to support its effective governance. Digital transformation is an effective option for realizing the modernization of national innovation governance capacity and promoting the building of an innovation-oriented country. Starting from the practical and research background of digital transformation of innovation governance， it analyzed how big data affected national innovation governance from five dimensions： multi-actor participation， scientific quality and transparency， accuracy， efficiency， and risk management capability. In addition， it categorized the application of big data in the national innovation governance system with five dimensions： science and technology development monitoring， foresight and strategy planning， project management， scientific activities mapping， policy evolution and its effect tracking. Finally， it put forward suggestions on how to make full use of big data in innovation governance and realizing the digital transformation of innovation governance： transform the government's innovative governance concept and model， establish a multi-level innovation-monitoring data integration platform， open up multi-level innovative information between departments， promote and implement the disclosure of innovation information， establish a sound legal system of innovation data management， and accelerate the construction of new digital infrastructure. It provides a basis for further understanding the important role of big data in innovation-led development and modernization of national governance system.