Objective To investigate the spectrum of diseases and the current situation of antibiotic use in rural hospitals and community health service centers in Chengdu, so as to provide evidence for selecting essential medicines and promoting rational use of antibiotics. Method We selected 7 township/community health institutions, from which we collected inpatient and outpatient information. Information about antibiotic use was also collected, including categories, cost, and dosage. A standard questionnaire was used to investigate physicians’ prescription behavior for principal diseases. Result Urban and rural areas had different spectrums of diseases. The major diseases in urban areas included diabetes mellitus, hypertension, chronic obstructive pulmonary disease, and respiratory tract infection; while those in rural areas were infectious diseases of the respiratory system, digestive system, and urinary system. The physicians’ prescription behavior was mainly based on their personal experience. Antibiotics accounted for 30-50% of the total medicine cost. The top four types of antibiotics with the highest cost were cephalosporins, penicillin, quinolones, and macrolides. Conclusion Based on the different spectrums of diseases, essential drug lists and standard treatment guidelines appropriate for rural health care should be developed to improve the rational use of drugs. Factors such as the average cost of daily dose and the course of treatment should be taken into consideration to reduce the overall cost of medicine. An antimicrobial resistance monitoring system and special training courses on rational use of antibiotics should be utilized in the rural health institutions.