Objective: To propose countermeasures and suggestions for the current predicament of pharmacy coherence among the upper and lower institutions in China's medical consortium. Methods: Based on the statistical analysis monitoring data on Hierarchical Diagnosis System and the medical alliance construction, the text analysis was conducted on the base of field research interviews and cases, the predicament of pharmacy coherence among the upper and lower institutions in China's medical consortium was raised. Results: The proportion of compact medical consortia which carried out policy requirements of pharmacy coherence was relatively low, and the policy implementation was better in towns than that in cities. The major quandaries include the difficulties of unifying medication catalogue and regional logistics, the limitations of medical insurance and drug administration policies, and the insufficient awareness of pharmacy coherence. Conclusions: Based on the practical experience in those areas, it is necessary to coordinate the policy of drug supply in compact medical consortia. The leading hospitals should establish the pharmaceutical management system and develop related rules and regulations, strengthen the capacity of pharmaceutical care, and implement shared medication information of patients among the institutions in the consortia.