The article constructs a theoretical framework of how national audit increases public expenditure efficiency by the revealing function, punitive function and recommendation function. Based on the input-oriented super efficiency DEA model, the paper calculates the public expenditure efficiency of 31 provinces in China from 2008 to 2013 and analyzes how the national audit increases public expenditure efficiency by using two-stage framework of DEA-Tobit. The results of statistical analysis show that the national audit does have a significant impact on the public expenditure efficiency through the synergistic effect among the revealing function, punitive function and recommendation function.