Sonneratia × hainanensis, a species once endemic to Hainan Island in China, is now endangered. China’s State Forestry Administration lists this species as a wild plant species with an extremely small population. Field fixed-point investigations, artificial pollination, and laboratory experiments, as well as other methods, were applied to study the reproductive system and seed germination of S. × hainanensis to elucidate the reasons for the endangerment of this species. The results are as follows: (1) Outcrossing index, pollen-ovule ratio, and artificial pollination showed S. × hainanensis has a mixed mating system and mainly focuses on outcrossing with some self-compatibility. (2) Fruit and seed placement tests showed that the fruit predators on the ground were mainly Fiddler crab and squirrel, with the predation rates being 100%. The artificially spread seeds do not germinate under natural conditions. The mean seed destruction rate and remaining rate of were 82.5% and 17.5%. (3) Seeds need to germinate under ambient light conditions, with an optimal photoperiod of 12 h. Seed germination is extremely sensitive to low temperatures because of optimum temperatures from 30 °C to 40 °C. At an optimal temperature of 35 °C, the seeds germinate under salinities ranging from 0‰ to 7.5‰, with an optimal salinity of 2.5‰, which shows the sensitivity of seed germination to salinity, with low salinity promoting germination, whereas high salinity inhibits germination. These findings indicate that the limited regeneration of S. × hainanensis is caused by the following: (1) Pollen limitation and inbreeding recession caused by the extremely small population of S. × hainanensis. (2) Seeds near parent trees are susceptible not only to high fruit drop rate, but to high predation beneath the parent trees′ canopy as well. (3) Seed germination has weak adaptability to light, temperature, and salinity.