Objective: The COVID-19 pandemic has challenged the health system worldwide. This study aimed to assess how China’s hierarchical medical system (HMS) coped with COVID-19 in the short-and medium-term. We mainly measured the number and distribution of hospital visits and healthcare expenditure between primary and high-level hospitals during Beijing’s 2020–2021 pandemic relative to the 2017–2019 pre-COVID-19 benchmark period. Methods: Hospital operational data were extracted from Municipal Health Statistics Information Platform. The COVID-19 period in Beijing was divided into five phases, corresponding to different characteristics, from January 2020 to October 2021. The main outcome measures in this study include the percentage change in inpatient and outpatient emergency visits, and surgeries, and changing distribution of patients between different hospital levels across Beijing’s HMS. In addition, the corresponding health expenditure in each of the 5 phases of COVID-19 was also included. Results: In the outbreak phase of the pandemic, the total visits of Beijing hospitals declined dramatically, where outpatient visits fell 44.6%, inpatients visits fell 47.9%; emergency visits fell 35.6%, and surgery inpatients fell 44.5%. Correspondingly, health expenditures declined 30.5% for outpatients and 43.0% for inpatients. The primary hospitals absorbed a 9.51% higher proportion of outpatients than the pre-COVID-19 level in phase 1. In phase 4, the number of patients, including non-local outpatients reached pre-pandemic 2017–2019 benchmark levels. The proportion of outpatients in primary hospitals was only 1.74% above pre-COVID-19 levels in phases 4 and 5. Health expenditure for both outpatients and inpatients reached the baseline level in phase 3 and increased nearly 10% above pre-COVID-19 levels in phases 4 and 5. Conclusion: The HMS in Beijing coped with the COVID-19 pandemic in a relatively short time, the early stage of the pandemic reflected an enhanced role for primary hospitals in the HMS, but did not permanently change patient preferences for high-level hospitals. Relative to the pre-COVID-19 benchmark, the elevated hospital expenditure in phase 4 and phase 5 pointed to hospital over-treatment or patient excess treatment demand. We suggest improving the service capacity of primary hospitals and changing the preferences of patients through health education in the post-COVID-19 world.