Objective Investigated the payment methods of 5 kinds of chronic diseases in public hospitals of Heze. Methods 8383 cases of Hypertension, diabetes, coronary heart disease, chronic bronchitis and hepatitis B were enrolled from The Municipal Hospital, The Second People’s Hospital, The Third People’s Hospital, The City Hospital of Traditional Chinese Medicine and The Infectious Disease Hospital in Heze. The information of medical records and the cost of hospitalization were collected and analyzed. Results The total hospitalization expense, examination fees and other costs of medicare patients were significantly higher than those of the non-medicare patients (P < 0.05), while the drugs expense was significantly lower than that those of non-medicare patients (P < 0.05). As to the medicare patients, hospitalized expense of male patients was significantly higher than that of female (P < 0.05), hospitalized expense and insurance expense of patients over 45 were significantly higher than those of patients under 45 (P < 0.05), hospitalized expense and insurance expense of patients retired were significantly higher than those of patients on-the-job (P < 0.05), total expense of urban patients were significantly higher than those of rural patients (P < 0.05). Conclusion Methods of payment of patients with chronic diseases was in relation with hospitalization expenses, which was also related to the social economic characteristics, but it is worth paying attention to avoiding excessive medical treatment and waste of resources, which need to take comprehensive measures in combination with social situation.