Phoebe zhennan S. Lee is a rare and endangered tree species in China, a nationally protected secondary plant. It is mostly scattered in the wild in subtropical evergreen broad-leaved forests below 1500 m above sea level. As the primary populations are almost destroyed, the existing resources are limited and scattered. Karst habitat has exposed rocks, shallow and barren soil and frequent drought. In theory, it is not suitable for the growth and seedling regeneration of P. zhennan, which likes humidity, shade and acid soil. Therefore, it may be difficult to renew the natural P. zhennan population in karst habitats in Dazu District and Yongchuan District of Chongqing. To explore the survival status and distribution model of the two P. zhennan populations, the field survey method is used to analyze the structure and the dynamic law of the populations and their quantity, by assessing the diameter structure, static life table, survival curve, structural dynamics and distribution pattern. It is hoped that the future development trend of the population can be predicted, and the theoretical basis for the protection, community renewal and vegetation restoration of the karst area will be provided. The results showed that:(1) the age structure of P. zhennan population in Dazu District tended to be a stable type, while it was an increase type in Yongchuan District. Both areas had abundant seedlings but with high mortality rates. (2) The individual numbers of both populations of P. zhennan generally decreased with the diameter class increased. The life expectation of the two P. zhennan populations fluctuated between different diameter classes. It was the highest in the diameter class Ⅱ in the population of P. zhennan in Dazu District, while it highest in the diameter class Ⅳ in Yongchuan District.(3) Both populations had Deevey-Ⅲ type survival curves, that was, the mortality of young trees was relatively high, and a relatively low population growth rate. (4) The population in Dazu District was randomly distributed, while that of the Yongchuan District was consolidated. P. zhennan were clustered populations at the growth and development stage, but their strength weakened with the growth of the age group. The population of P. zhennan in the karst region had a long growing time, a strong capacity for natural regeneration but sensitive to external disturbances. It is suggested to enhance seedling selection and improve seedling survival to promote natural renewal and restoration of P. zhennan population.