Positive interactions, such as facilitation and mutualism, can promote community construction and maintenance of ecosystem biodiversity and resilience. However, there are few global meta-analyses on whether and how facilitative interactions affect biodiversity indices in terrestrial and aquatic ecosystems. We synthetically reviewed 344 studies of the effects of facilitative interactions on biodiversity, and reviewed and meta-analyzed 177 studies, which contain available data about the effects of facilitative interaction on ecosystem biodiversity, richness, and abundance. The results indicated an upward trend for the number of studies published annually on this topic, particularly after 2010, reflecting an increasing interest in facilitative interactions. Most studies were conducted in North America and Europe, followed by South America, Asia, Oceania, and Africa. Most studies were conducted in marine and coastal ecosystems and grasslands, followed by forests, shrublands, deserts, and inland wetlands. Our meta-analyses showed that facilitative interactions significantly increased the Shannon diversity, species richness, and species abundance in various terrestrial and aquatic ecosystems, even if several studies showed non-significant or negative effects. Facilitators promoted species biodiversity mainly by reducing physical or biotic stress, ameliorating harsh environments, spreading pollen, providing shelter, and defending against enemies. We conclude that facilitative interactions are essential in maintaining and promoting the biodiversity of various ecosystems. Thus, the conservation of facilitator species should be a priority, and facilitative interactions should be applied to ecosystem restoration and management.