Due to the inherent limitations of underground spaces, such as the lack of natural ventilation and sunlight, underground space users tend to face more health risks compared with their aboveground counterparts. However, little is known about how the underground environment, users’ health, and their associations were impacted by the outbreak of the pandemic. In this study, we investigated and compared the impacts of the general underground environment on regular users’ physical and psychological health before and after the pandemic. To achieve this aim, the data from 525 surveys were collected from eleven underground sites, followed by an objective field measurement study conducted at five underground sites in Hong Kong pre- and post-outbreak of the pandemic. The multigroup structural equation modelling results indicated that: (i) surprisingly, the users’ satisfaction towards almost all underground environment factors, including greenery, connectivity with the aboveground environment, thermal comfort, ventilation, indoor air quality, acoustic comfort, and lighting, excluding wayfinding, were significantly higher in the post-outbreak period; (ii) the users’ health, both physical and psychological, was significantly better in the post-outbreak period; (iii) the impacts of visual comfort on the users’ physical and psychological health were significantly greater in the post-outbreak period (critical difference ratio (|CDR|) > 1.96); (iv) the impacts of wayfinding, greenery, and acoustic and thermal comfort on the users’ physical or psychological health were significant only in the pre-outbreak period (|CDR| > 1.96); (v) the impacts of connectivity on the users’ physical and psychological health were significant in both the pre- and post-outbreak periods (|CDR| < 1.96). The findings were further cross-validated using the objective measurement results. With an increasing need to develop healthy underground spaces, the study contributes to the development, design, and management of the underground environment to enhance the users’ health in the post-outbreak era.