In order to improve the operation quality of the cross-enterprise batch management system in the tobacco industry, a comprehensive data quality index evaluation model is proposed in this paper. By analyzing the characteristics of batch management data, 7 indicators are selected to evaluate the system data, and the influence of human factors is eliminated by the combination weight determined by the analytic hierarchy process (AHP) and entropy weight method (EWM). The proposed evaluation model is applied to the quality assessment of the actual statistical data of Zhejiang Tobacco Industries Co. and six cooperative production enterprises in the cigarette industry. The results show that the model can scientifically evaluate the system data quality of each enterprise, intuitively rank the data quality of various enterprises, and truly reflect the change trend of data quality, indicating the feasibility and effectiveness of the model. This method can provide support for improving the data quality level of the cross-enterprise batch management system.