The outbreak of COVID-19 has caused unprecedented disruptions to public transportation services, passengers' mode choice preferences, and their behavioral pattern. Recent studies have updated the systemic shift from shared travel to private mode due to the perceived higher health risk of shared mobility. However, findings from these studies may not be applicable to public transport-oriented cities with very low rate of private car ownership. In the long term when we arrive at a stabilized ‘New Normal’, the need to promote public transport is likely to be re-emphasized with high priority. This study presents insights into the factors affecting public transport (PT) preferences and potential modal shifts within various modes of PT when proactive and reactive health control measures are implemented. An online stated preference survey was conducted in Hong Kong, where public buses, public light buses, MTR, and taxis are the popular modes of public transport. The regret-based panel mixed multinomial logit model was applied in this study, aiming to capture individual’s regret aversion psychology in the context of the COVID-19 pandemic. The results of our random regret model suggest that travelers generally have lower regrets for the chosen mode when having passenger temperature screening, COVID tracing app, and more frequent disinfection, while seem to be unaware of the in-vehicle air quality. Interaction effects between health control measures and personal characteristics (e.g., age and risk attitudes) were also considered. Trip characteristics, including in-vehicle crowding level, fares, in-vehicle travel time, waiting time at a station, walking time, and trip purpose, were found to influence passengers' choices of travel modes. Policy simulations of possible changes in public transport modal preferences in the presence of various health control measures have also been undertaken. The findings suggest that overall health control measures are appreciated by passengers and do align with promotion of a return to public transport use. However, their effects are quite moderate and should be selectively used for different transport modes. Increasing service frequency can be a promising solution, which reduces crowding and waiting time of passengers using public transport modes, and reduces virus transmission risk. This study contributes to a better understanding of public acceptance and preference toward health control measures in public transport, and call for in-depth cost-benefit analysis in the related fields so that better response can be made in possible future public health crisis.