The endangered mangrove Scyphiphora hydrophyllacea is found in China only in Hainan’s intertidal zones. Its populations are declining severely due to anthropogenic disturbances and regeneration failure. To clarify its environmental adaptation mechanisms, we investigated the effects of temperature, light intensity, photoperiod, salinity, soil, and flooding cycle on seed germination, seedling growth, and physiological traits, revealing that (1) the optimal germination conditions for seeds were 30–35 °C, 24 h continuous illumination at 25,000 lux, and 0‰ salinity, with soil type showing no significant effect (p > 0.05); (2) seedlings at 1–2 months post-germination achieve maximal growth at 30 °C in non-saline conditions, with salinity suppressing growth and light intensity affecting only crown expansion; and (3) flooding responses are age-dependent: seedlings at 1–2 months post-germination show optimal growth at 8 h per day (100% survival), while 12 h (h) per day reduces survival by 13.3%. One-year-old seedlings exhibit distinct strategies: 4 h per day flooding induces escape responses (peak growth, chlorophyll, sugars), 8 h per day shows photosynthetic compensation despite metabolic trade-offs, and 12 h per day triggers tolerance mechanisms (biomass maximization via structural reinforcement). These findings demonstrate S. hydrophyllacea’s multifactorial adaptation to intertidal conditions, providing critical physiological benchmarks for conservation strategies targeting this threatened ecosystem engineer.