Using data of 35 industries in the 30 regions from 2000 to 2012, the paper studies the impact of social capital and government intervention on the regional capital allocation efficiency. The research finds the following conclusions after empirical tests: (1) capital allocation efficiency is higher in the regions of higher social capital and lower government intervention. (2) further study found that social capital and government intervention are alternative in influencing the efficiency of capital allocation; the impact of social capital on regional capital allocation efficiency is more significant in the areas of higher government intervention. This research provides a theoretical explanation and empirical support for differences in the regional capital allocation efficiency from the informal system perspective.