China introduced a series of health reforms in 2009, including a national essential medicines policy and a medical insurance system for primary care institutions. This study aimed to determine the changing prescribing patterns associated with those reforms in township hospitals.A multi-stage stratified random cluster sampling method was adopted to identify 29 township hospitals from six counties in three provinces. A total of 2899 prescriptions were collected from the participating township hospitals using a systematic random sampling strategy. Seven prescribing indicators were calculated and compared between 2008 and 2013, assessing use of medicines (antibiotics and adrenal corticosteroids) and polypharmacy, administration route of medicines (injections), and affordability of medicines.Significant changes in prescribing patterns were found. The average number of medicines and costs per-prescription dropped by about 50%. The percentage of prescriptions requiring antibiotics declined from 54% to 38%. The percentage of prescriptions requiring adrenal corticosteroid declined from 14% to 4%. The percentage of prescriptions requiring injections declined from 54% to 25%. Despite similar changing patterns, significant regional differences were observed.Significant changes in prescribing patterns are evident in township hospitals in China. Overprescription of antibiotics, injections and adrenal corticosteroids has been reduced. However, salient regional disparities still exist. Further studies are needed to determine potential shifts in the risk of the inappropriate use of medicines from primary care settings to metropolitan hospitals.