Based on the supervision of government audit on the distribution of fiscal subsidies, this paper studies whether government audit can effectively promote the role of fiscal subsidies in promoting enterprise innovation. This paper finds that government audit can play a deterrent effect, reduce the mismatch degree of financial subsidies, and thus enhance the role of fiscal subsidies in promoting innovation investment of enterprises. The deterrent effect of government audit is subject to the legal environment. Only in regions with good legal environment can government audit effectively play a deterrent effect, which can enhance the role of fiscal subsidies in promoting enterprise innovation. This paper provides the micro evidence of the role of government audit in the national innovation and development strategy, which has some enlightenment on how to further enhance the role of government audit.