The economic order governance function of national audit has played a great role in helping the new development pattern of economic double cycle and improving the efficiency of regional innovation. Taking the provincial panel data from 2006 to 2019 as the research sample, based on the joint test method of simple intermediary effect model and multiple intermediary effect model, this paper studies the influence of national audit on regional innovation efficiency and the intermediary role played by the new economic dual-cycle development pattern. The results show that the comprehensive efficiency of national audit has significantly promoted the improvement of regional innovation efficiency, and the internal and external economic circulation has played a dual intermediary role. Further research found that in the process of national audit promoting regional innovation efficiency by helping to form a new development pattern, special attention should be paid to the influence of government debt risk and regional digital construction differences.