As awareness grows regarding the impacts of sea-level rise on mangroves, research investigating the physiological response of mangroves to flooding stress has increased. However, the understanding of the transcriptional-level response remains limited. Mangrove survival is threatened by increased inundation time caused by sea level rise. Several studies have been conducted to reveal the response mechanisms of mangrove plants to tidal inundation, but these studies have primarily focused on growth and physiological changes, with fewer studies on the transcriptomics of the mangrove species K. obovata in response to tidal inundation, particularly in terms of hormonal signaling and transcription factors. In this study, we used transcriptomics to resolve the effects of flooding stress on key metabolic pathways and differentially expressed genes in K. obovata, as well as to clarify changes in physiological, biochemical, and complex molecular mechanisms in K. obovata under different flooding stresses, which has theoretically established the groundwork for the development of new varieties of flood-tolerant K. obovata, as well as for mangrove conservation and management.