At present， the policy operation of compact county medical alliances in our country is facing difficulties. In order to deeply analyze the difficulties existing in the policy operation of compact county medical alliances， the six factors of Meter?Horn model were used as the framework for analysis， which were policy objectives and standards， policy resources， organization communication and operation activities， operating organization characteristics， operating environment and operator value orientation. The results showed that dilemmas of policy operation included a wide range of policy objectives， a long time for implementation of policy standards， low efficiency in the allocation of health resources， weak effect of medical insurance payment， and unsmooth referrals in the tiered system of diagnosis and treatment， unmatched information construction， insufficient capacity of primary health care institutions， and the low level of coordination between medical services， medical insurance and pharmaceuticals. In order to solve the dilemmas of policy operation of compact county medical alliances， the following suggestions were proposed to promote the stable construction and long?term development of compact county medical alliances. Specific and feasible policies should be formulated. The allocation of medical resources should be optimized. Information exchange and sharing should be realized. The primary health care capacity should be improved. The medical insurance reform should be strengthened.