In order to deal with the mixed multi-criteria decision making problem with unknown criteria weight, a hybrid multi-criteria decision making method based on minimum cross entropy and vertical distance is proposed. The mixed decision information is normalized and processed by the normalized methods of different types of evaluation information, the objective weight of each criterion is determined by the information entropy method, single-valued utility function reflects the subjective judgment of each decision maker on the importance of different criteria, and the subjective weight of each criterion of each decision maker is obtained. Based on the minimum cross entropy, the subjective combination weight of each criterion is obtained by integrating the subjective weights vector of each criterion. An optimization model is constructed to minimize the sum of the cross entropy between criterion’s comprehensive weight and subjective weight vector, and objective weight vector. Thus, the comprehensive weight vector of each criterion is determined. The ranking of the alternatives is obtained by the vertical distance between the alternatives and the positive or negative ideal solutions. Finally, the hybrid decision- making method is applied to the optimization of innovative projects in Henan Pilot Free Trade Zone, and the validity and feasibility of the decision making method are verified by comparative analysis.