Accessibility research of healthcare facilities is developing towards multiple transportation modes (MTM), which are influenced by residential transportation choices and preferences. Due to differences in travel impact factors such as traffic conditions, origin location, distance to the destination, and economic cost, residents’ daily travel presents different residential transportation mode choices (RTMC). The purpose of our study was to measure the spatial accessibility of healthcare facilities based on MTM considering RTMC (MTM-RTMC). We selected the gravity two-step floating catchment area method (G2SFCA) as a fundamental model. Through the single transportation mode (STM), MTM, and MTM-RTMC, three aspects used to illustrate and redesign the G2SFCA, we obtained the MTM-RTMC G2SFCA model that integrates RTMC probabilities and the travel friction coefficient. We selected Nanjing as the experimental area, used route planning data of four modes (including driving, walking, public transportation, and bicycling) from a web mapping platform, and applied the three models to pediatric clinic services to measure accessibility. The results show that the MTM-RTMC mechanism is to make up for the traditional estimation of accessibility, which loses sight of the influence of residential transportation choices. The MTM-RTMC mechanism that provides a more realistic and reliable way can generalize to major accessibility models and offers preferable guidance for policymakers.