The rural three-tier healthcare system is an essential part of the Chinese healthcare service system. To ensure rural residents’ equal access to such healthcare services, it is necessary to examine the current status of the healthcare system in rural China and formulate corresponding improvement suggestions. This study therefore collects the data from the China Health Statistics Yearbook, the China Health Yearbook and the China Statistical Yearbook between the years 2004 and 2021 to calculate the Gini coefficient (G), health resource density index (HRDI) and Theil index (T) first, and then perform the Mann–Kendall test afterwards to evaluate the equity of healthcare resource allocation comprehensively. This series of analysis helps in drawing the following conclusions: (1) county and county-level city medical and health institutions (CMHIs) show a higher development trend in comparison with township hospitals (THs) and village clinics (VCs); (2) VCs have higher institutional fairness, while for beds and personnel, CMHIs and THs are more fairly positioned; (3) more specifically for CMHIs and THs, personnel allocation is more fair than beds and institution allocations; (4) the density of healthcare resources in the eastern and central regions is higher than that in the western part, while the intra-regional distribution of beds and personnel in the west and central regions is better than that in the eastern region; (5) intra-regional differences are more significant than inter-regional differences and the fairness according to population distribution is higher than that of geographical area allocation. The results of this study provide theoretical basis for further optimizing the allocation of healthcare resources and improving the fairness of healthcare resources allocation from a macro perspective.