In this paper, the DEA model is improved, so that through the optimization of key resources we can minimize the key inputs, or maximize the important output, or optimize the both simultaneously. The improved DEA model is used to optimize t the allocation of resources and adjust the efficiency of innovation. The research shows that：(1)When the target is the minimization of the key inputs, the optimal allocation of single key resource can be more targeted and more economical; the optimal allocation of multiple key resources can meet different needs but also reduce the optimized space of individual resources. (2) When the target is the maximization of the important output, it can also be achieved by optimizing the allocation of key resources, but due to the increase in important output, compared to the case (1), it sacrifice some critical resources to reduce the space.(3) When the objective is to minimize the critical inputs and maximize the critical outputs, the objective also can be achieved through the allocation optimization of key resource, and the key resources of the optimization space is different from the first two.(4) When we achieve the above three goals through the optimization of key resources, the evaluated enterprise are improved from non DEA effective unit to DEA effective unit.