Control performance of the industrial process is inevitably influenced by the measurement noises and non-Gaussian external disturbances. This influence has not been fully considered in the traditional variance-based controller design. To reduce the influence, a novel scheme that can enhance the control performance is developed by integrating dynamic data reconciliation (DDR) into minimum rational entropy control (MREC) in this paper. Firstly, the influence of measurement noise is fully considered, and a novel DDR method is proposed to deal with the minimum entropy control (MEC) process such that the influence of measurement noise can be reduced, and the control performance will be improved. Then, based on the DDR-MREC performance index, a benchmark for evaluating the control performance of non-Gaussian systems is established. Finally, the proposed control performance assessment (CPA) method is applied to the wind energy conversion system and compared with the CPA method based on DDR-minimum variance control. The experimental results have demonstrated that the proposed new method is more effective than existing works.