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Abstract Background In 2009, the Chinese Central Communist Party and the China State Council started to implement comprehensive healthcare reforms. The first round of reforms, involving Anhui province, was from 2009 to 2011, and focused on primary healthcare institutions. This study conducts an initial assessment of the effects of specific parts of the reforms in Anhui. Methods Mixed quantitative and qualitative methods were adopted for data collection. Seven hundred and three health institutions from 15 counties were randomly chosen. The practices, development, effects, problems, and other relevant information related to the reform were classified into four aspects: medicine management; personnel systems and income distribution mechanisms; compensation mechanisms for primary healthcare institutions; and strengthening the primary healthcare system. The effects of reform were analyzed by evaluating changes in compensation channels, visit costs, diagnosis and treatment structure, hardware, structures, efficiency, and behavior. Results A new system for authorizing drugs resulted in a total of 857 new drugs being accessible at agreed prices through primary healthcare institutions in Anhui. The cost of the average outpatient visit decreased from 35.29 RMB to 31.64 RMB, although for inpatients, the average cost increased from 799.05 RMB to 992.60 RMB. The number of healthcare personnel decreased, but their workloads increased. The total revenue from government sources increased by 41.09%, and the proportion of revenue from drugs decreased by 25.19%. The rate of diagnosis and treatment visits and outpatient visits to primary healthcare institutions increased. Finally, between 2008 and 2010, 1,195 standardized township hospitals, 14,134 village clinics, and 1,234 community health service institutions were constructed. Conclusion The reform of primary healthcare institutions in Anhui has improved the personnel structures surrounding frontline healthcare workers, increased their incomes, improved work efficiency, and changed the compensation patterns of primary healthcare institutions, improved hardware, reduced drug prices, and, to some extent, improved the diagnosis and treatment structure. However, the reforms have not radically changed the behavior of medical workers or the visit patterns of patients. Approaches such as strengthening performance evaluation, and carrying out initiatives to further mobilize frontline healthcare workers, enhance rational drug use through improved training and educate patients, should be undertaken in the future.