The Tibetan Plateau, a vulnerable eco-region for global warming, has huge value of science and practice on ecological restoration to mitigate and adapt to climate change. Sophora moorcroftiana shrubs, which are widely distributed in the middle reaches of Yarlung Zangbo River basin, have been recovered on desertified land benefiting from natural restoration during the past decades. However, the effects of habitat conditions in different topographies on population structure and distribution of S. moorcroftiana have been rarely reported. Here, we achieve the variation of vegetation and micro-topography of S. moorcroftiana population by a series of field surveys with Terrestrial Laser Scanning (TLS) during natural restoration in 2017. The results indicate that the positive correlation between height and CPA reached the 99% confidence level (p < 0.01). The plant height was significantly correlated with the elevation and slope (r = 0.167 and 0.145, respectively; p < 0.01). While the distribution of S. moorcroftiana population decreased along increasing elevation, and the trend of distribution was decreasing firstly, increasing secondly and decreasing finally with increasing slope. The habitat conditions on the southwest slope of approximately 20°-25° with altitudes of 3593-3643 m most favor to the distribution of S. moorcroftiana population in this region. These will help to understand the effect of micro-topography on population structure and distribution of Sophora moorcroftiana in southern Tibetan Plateau and assess the effectiveness of natural restoration of Sophora moorcroftiana in different topographies.