Based on the related data of large scale industrial enterprise input from 2009 to 2015, this paper uses super-efficiency DEA model and DEA-Tobit model to make empirical analysis on the impact of enterprise’s basic research on enterprise innovation efficiency. The results showed that the enterprise innovation efficiency in eastern-and-coastal provinces is significantly higher than that in central-and-western provinces. As time goes by, the differentials are diminishing. Secondly, the impact of enterprise’s basic research on enterprise innovation efficiency is lagging. The longer the lag phase, the more significant the effect will. This is also the reason why the enterprises dislike basic research. Furthermore, government R&D investment and enterprises’ research investment have no significant effect on the output of basic research. Thus the corresponding countermeasures and suggestions are put forward. Except for the financial support, government policy guidance is more is more important.