Background: The full coverage policy for essential medicines (FCPEMs) was proposed and implemented in Taizhou city of Zhejiang Province of China to promote equal access and adherence to medicines. This study aimed to examine the effects of FCPEMs on the inequality in medication adherence among local patients with hypertension and diabetes, and to explore their influencing factorsMethods: We collected electronic health records of patients with hypertension and diabetes of three districts of Taizhou from 2011-2016. With the implementation time of FCPEMs being different, we applied a retrospective longitudinal study design and selected the records of 1 baseline year before and 3 follow-up years after following the implementation of FCPEMs. All data entries of the same patient were aggregated and generated a dataset with 4-year longitudinal data. The concentration index (CI) and its decomposition method were employed to measure the factors contributing to inequality in medication adherence and the role played by FCPEMs.Results: The sample size of the 4 years retrospective longitudinal data rose from 264,836 to 315,677, 340,512 and 355,676 individuals and the proportion of the patient taking the free medicines were 17.6% to 25.0% and 29.8% after FCPEMs. The proportion of patients with high adherence increased from 39.9% to 51.6%, 57.2%, 60.5% and CI changed from 0.073 to -0.011, -0.029, -0.035, where the rate of the contribution of FCPEMs were 54.792%, 1.223% and -19.092% and ranked 2nd, 7th and 2nd after the implementation of FCPEMs. The changes in CI of medication adherence for every two years were -0.084, -0.018, -0.006, and the contribution of FCPEMs were -0.006, 0.006, 0.007, ranking the 2nd, 2nd and 1st and mainly attributed to the changes of CI of FCPEMs.Conclusions: The medication adherence of patients with hypertension and diabetes improved after the implementation FCPEMs in Taizhou, but the inequality did not show a consistent rate of improvement. In general, FCPEMs contributed to improvements in the inequality in medication adherence. FCPEMs could be a protective factor against the income-related inequalities, but this would need further investigations and to be accompanied by other systematic efforts.