Negative distance-dependence of conspecific seedling mortality (NDisDM) is a crucial stabilizing force that regulates plant diversity, but it remains unclear whether and how fragment size shifts the strength of NDisDM. Here, we surveyed the seed‒seedling transition process for a total of 25,500 seeds of a local dominant tree species on islands of various sizes in a reservoir and on the nearby mainland. We found significant NDisDM on the mainland and large and medium islands, with significantly stronger NDisDM on medium islands. However, positive distance-dependent mortality was detected on small islands. Changes in distance-dependence were critically driven by both rodent attack and pathogen infestation, which were significantly affected by fragment size. Our results emphasized the necessity of incorporating the effects of fragment size on distance-dependent regeneration of dominant plant species into the existing frameworks for better predicting the consequences of habitat fragmentation.