Abstract: Innovation is a key element for start-ups. As the institutional arrangement of enterprises, internal control is crucial to the innovation efficiency of start-ups. Based on the panel data of GEM from 2014 to 2018, this paper empirically analyzes the impact of internal control on the innovation efficiency of start-ups, and employs the executive power as the threshold to test relationship between internal control and innovation efficiency of start-ups. The results show that internal control has a positive effect on the innovation efficiency of start-ups, and that executive power has double threshold effect. Only in the middle level of executive power range can internal control play the strongest positive role in innovation efficiency. After further testing situational effect of the four dimensions of executive power, it is found that executive organizational power and ownership power show a single-threshold effect. Based on the above research, suggestions are put forward from the perspectives of internal control and executive power.