Objective To provide basis to improve the ability of primary care services in Chengdu by comparatively analyzing inpatient medical service of primary medical institutions (community health service centers and township health centers). Methods From October to November 2016, the data of inpatient services in primary medical institutions in Chengdu, including 390 primary medical institutions in 22 districts (cities) and counties, were investigated by questionnaire. SPSS 19.0 was used for data collection and analysis, while the univariate logistic regression and multiple logistic regression were used to analyze the influencing factors. Results It was more common for rural primary medical institutions to carry out inpatient medical services than urban (96.18% vs. 53.84%). The coverage rate of insurance in urban areas was higher than rural areas (98.41% vs. 90.87%), while the rate of adopting clinical pathway of single disease was quite low both in urban areas (23.81%) and rural areas (18.25%). Primary medical institutions in urban areas launched more special projects of inpatient services than those in rural areas (14.29%–17.46% vs. 3.57%–7.54%). The total amount of inpatient medical services in 2015 in rural areas was larger than urban areas (529 611 vs. 103 912), the total number of inpatient services in rural was 5.09 times that in urban primary medical institutions, the average inpatient services in 2015 per one rural primary medical institution was 1.27 times that in urban, per 10 000 residents in rural areas consumed 3.01 times more inpatient medical services than those in urban areas in average, the median beds utilization efficiency in rural areas was better than in urban areas (74.47% vs. 22.47%); work intensity of inpatient medical service in rural areas was greater than in urban areas (234.57 vs. 81.74 cases per year per doctor). The number of inpatient services was positively related to population in service (when less than 100 000 residents), inpatient beds, the number of drugs, the number of medical staff. Conclusions For inpatient medical service, there are obvious differences between urban and rural areas in Chengdu. Therefore, above differences should be taken into full consideration in the allocation of resources in primary medical institutions. Thus more targeted management measures should be formulated.