In order to achieve precise control effect of greenhouse environmental factors, an innovative optimization control system arithmetic based on CFD was presented. By using orthogonal experiment in DOE, controller design in the optimal system was obtained, meanwhile, iteration times of CFD could be reduced as soon as possible. Taking control temperature field as an example, through setting up temperature distribution index and making its minimum by the strategy of using iterative algorithm with CFD calculated, the difference of temperature distribution could be decreased. The greenhouse comprehensive production efficiency was improved. Lastly, an experiment was illustrated by proposed method. The results showed that the algorithm was proved to achieve the control law easily. 