The costliness index (CI) is an index that is used in various ways to improve the quality of medical care and the management of appropriate treatment in medical institutions. However, the current calculation method for CI has a limitation in reflecting the actual medical cost of the patient unit because the outpatient and inpatient costs are evaluated separately. It is desirable to calculate the CI by integrating the medical cost into the episode unit. We developed an episode-based CI method using the episode classification system of the Centers for Medicare and Medicaid Services to the National Inpatient Sample data in Korea, which can integrate the admission and ambulatory care cost to episode unit. Additionally, we compared our new method with the previous method. In some episodes, the correlation between previous and episode-based CI was low, and the proportion of outpatient treatment costs in total cost and readmission rates are high. As a result of regression analysis, it is possible that the level of total medical costs of the patient unit in low volume medical institute and rural area has been underestimated. High proportion of outpatient treatment cost in total medical cost means that some medical institutions may have provided medical services in the ambulatory care that are ancillary to inpatient treatment. In addition, a high readmission rate indicates insufficient treatment service for inpatients, which means that previous CI may not accurately reflect actual patient-based treatment costs. Therefore, an integrated patient-unit classification system which can be used as a more effective CI indicator is needed.