Magnolia ovoidea is a narrowly endemic, Critically Endangered tree with a fragmented distribution in south-west Yunnan, China. We examined the size structure of this species, documented threats and assessed its extinction risk. We found the species in six locations, all in unprotected areas, in Maguan County. The largest subpopulations are in Donggua Lin and Youfang Po, with 17 and 50 living individuals, respectively. The distribution of the diameter at breast height of the M. ovoidea population has an inverse J-shape, indicating a stable size structure. However, the distribution of the height of seedlings is L-shaped, suggesting inhibited regeneration. The natural vegetation is severely fragmented in all six locations, surrounded by roads, farmlands, and Alnus nepalensis or Cunninghamia lanceolata plantations. We recommend that M. ovoidea should be categorized on the IUCN Red List as Critically Endangered based on criteria B2ab(iii) + C2a(i).