Objective To estimate the cost of continuous renal replacement therapy (CRRT) in public hospitals and analyze the main influencing factors of the cost, in order to provide evidence for the optimal application of CRRT technology. Methods In March 2021, activity-based costing was used to estimate and analyze the cost of CRRT, the data of which were collected from 5 hospitals in Jiangsu, Zhejiang, Henan, Sichuan and Xinjiang, and single factor sensitivity analysis was used to find the main influencing factors of the cost. Results The hourly treatment costs of CRRT in the 5 hospitals ranged from 265.30 to 474.44 yuan, with an average of 376.81 yuan. The costs of manpower and filters accounted for the top two largest proportions, the manpower cost of continuous veno-venous hemofiltration and continuous veno-venous hemodiafiltration accounted for 22.90% and 21.51%, respectively, and the filters cost of the two types of CRRT accounted for 15.07% and 17.73%, respectively. The unit cost and cost composition varied greatly between hospitals. There were four factors affecting the unit cost, namely clinical operation, efficiency, price and patient, among which clinical operation difference was the primary factor leading to cost difference. Conclusions The application cost of CRRT technology varies greatly among hospitals, and there are many factors affecting the cost. Public hospitals face great pressure in cost control. It is necessary to strengthen the internal control operation management of public hospitals, establish CRRT clinical operation standards, and improve the quality of medical services in public hospitals.