Access to public health services is a cause that benefits the people and concerns the vital interests of the people. Everyone has access to basic health care services. The continuous improvement in people’s health is an important indicator of the improvement in people’s quality of life. This paper selects data from the European Union (EU) on aspects of public health expenditure, medical care resources, and government emergency coordination capacity from the period 2008 to 2017. Principal component analysis and factor analysis are used to measure their public health service capacity scores and conduct a comparative analysis. On this basis, the TOBIT model is adopted to explore the driving factors that lead to the spatial differentiation of public health service capabilities, and to combine it with the data of the COVID-19 epidemic as of 8 August 2020 from the official announcements of the World Health Organization and governments for further thinking. The results indicate that the public health service capacity of countries in the EU is showing a gradual increase. The capacity in Western Europe is, in turn, higher than that of Northern Europe, Southern Europe and Eastern Europe. In addition, the overall capacity in Western Europe is relatively high, but it is not balanced and stable, while Northern Europe has remained stable and balanced at a high level. Population density, degree of opening up, education level, economic development level, technological innovation level, and degree of aging have a positive effect on public health service capabilities. The level of urbanization has a negative effect on it. However, in countries with strong public health service capabilities, the epidemic of COVID-19 is more severe. The emergence of this paradox may be related to the detection capabilities of countries, the high probability of spreading thCOVID-19 epidemic, the inefficient implementation of government policy, the integrated system of the EU and the adverse selection of youth. This paper aims to improve the ability of the EU to respond to public health emergencies, improve the utilization of medical and health resources, and better protect people’s health from the perspective of public health service capacity.