Objective: The paper explores the effect of disease basic diagnosis and treatment module in the cost management and proposes its application. Methods: The clinical data of 103 children with respiratory infection/inflammation (< 17 years old) who received inpatient treatment before and after the application of basic diseases diagnosis and treatment module in the Second Affiliated Hospital of Guangxi University of Science and Technology were collected. The changes of length of stay, total hospitalization cost, drug cost, proportion of drug cost and rational use of antibiotics were analyzed before and after the application. Results: After using the disease basic diagnosis and treatment module to manage the cost, the length of hospitalization of DRG was 3d, the total hospitalization cost was 1799.23 yuan, the drug cost was 487.02 yuan, and the drug cost accounted for 32.47%, which were lower than or shorter than before 5d, 2429.85 yuan, 924.57 yuan, 39.02% (P < 0.05). The rationality of antibiotic use was 94.44%, which was higher than 81.63% before application (P < 0.05). Conclusion: Using disease basic diagnosis and treatment module for cost management can standardize clinical diagnosis and treatment behavior, improve medical service quality and achieve accurate management.