Most of the trees at treeline on the Tibetan Plateau are endemic to the Plateau. Yet little is known about these species. The study focused on the population structure, spatial patterns and associations of the treeline species Abies forestii var. georgei and Juniperus saltuaria at treeline and timberline in Mountain Baima Xueshan on the southeast Tibetan Plateau. These species form monodominant communities on the north- and south-facing slopes, respectively. Stem density, DBH-distribution, distribution pattern of different tree size classes, and intraspecific spatial association between different tree size classes of both species were analyzed. Spatial structure varied between A. forestii var. georgei and J. saltuaria, and for the same species, the spatial structures were also different from timberline to treeline. Stem density, mean tree height and young individuals of A. forestii var. georgei were significantly higher than those of J. saltuaria. For the same species, they were different from timberline to treeline, i.e., stem density and mean tree height of both species became lower. Size classes of both species were mainly clustered either at treeline or at timberline but at different scales, and spatial patterns of young J. saltuaria were mainly dominated by random patterns. Clumps of trees created more favorable microenvironments in harsh environments at treeline and timberline. Most tree size classes showed positive intraspecific spatial associations, but positive associations between size classes of J. saltuaria were not as significant as those of A. forestii var. georgei. The south-facing slope was usually subjected to varying intensities of pastoralism. Livestock disturbance greatly changed the microhabitat and reduced the number of young individuals. The potential of trees to regenerate was greatly inhibited, while A. forestii var. georgei showed greater regeneration potential. Spatial structures of J. saltuaria were also modified by this kind of human impact.