Polymer flooding has characteristics of high oil production rate and short production duration, complicated operation cost change rule, and its operation cost structure and prediction method are different from water flooding. Scientific prediction of polymer flooding operation cost is essential to control the cost of operations and establish a cost plan. Combining with the characteristics of polymer flooding development, this paper applied gray system theory and principal component analysis method to select the influencing factors, and then established prediction model to predict polymer flooding operation cost. The practical application proves that this method can be used to predict polymer flooding operation cost better and achieve the purpose of improving the prediction accuracy. It can provide a scientific basis for the rational preparation of development planning program.