Abstract: This paper takes the strategic emerging industries (SEI) as the research object to examines the impact of financial misallocation on the efficiency of government subsidies through the panel threshold model. The research finds that, (1) Government subsidies do not always promote the efficiency of corporate investment due to adverse selection and moral hazard; (2) Financial misallocation is a main environmental factor affecting the efficiency of government subsidies; (3) the effect of financial misallocation on government subsidies has significant asymmetric inverted "U" type and double threshold effect: if the misallocation in the left avertence areas, government subsidies have positive effect which can promote the corporate investment efficiency; if it in mildly bad areas, Government subsidies have a slight non efficiency effect; but if it in right avertence misallocation areas, government subsidies will not show significant efficiency results, leading to serious investment efficiency losses. This research confirm that the allocation of financial resources has a moderating effect on the policy guidance.