Unraveling the mechanisms causing restricted regeneration and limited distribution range has become a core issue for biodiversity conservation. Anthropogenic disturbances are changing a variety of ecological factors, but how their relative importance varies across multiple regeneration stages is still unclear even in a single species. In this study, we focused on Metasequoia glyptostroboides, a relict species suffering a severely restricted regeneration in the wild, and performed controlled experiments using 54,600 seeds to investigate seedling emergence and growth in both its natural and adjacent unoccupied habitats to disentangle the roles of seed availability, interspecific competition and herbivore/omnivore attack across early regeneration stages. Our results showed that these factors mainly exerted their predominant effects at initial regeneration stages. Compared with herbivore/omnivore attack, seed availability and interspecific competition were the crucial factors regulating seedling emergence. The first-year seedling survival rate was only significantly influenced by interspecific competition, and the survival of second-year seedlings was independent of all these factors. Moreover, we detected similar impacts of these factors in the adjacent unoccupied habitats to those in the natural habitats, indicating their roles in limiting population expansion. Our findings provide some suggestions to assist the natural regeneration and range expansion of M. glyptostroboides, and our experiment design can be applied in the assessment of endangerment causes for other endangered plants.