Background: The Himalayan forests are of great importance to sustain the nature and community resource demands. These forests are facing pressures both from anthropogenic activities and ongoing global climatic changes. Poor natural regeneration has been considered a major problem in mountainous forests. To understand the population structure and regeneration status of Larix (Larix griffithiana and Larix himalaica), we conducted systematic vegetation surveys in three high-altitude valleys namely Ghunsa (Kanchenjunga Conservation Area, KCA), Langtang (Langtang National Park, LNP), and Tsum (Manaslu Conservation Area, MCA) in Nepal Himalaya. The average values of diameter at breast height (DBH), height, and sapling height were compared for three sites and two species using Kruskal-Wallis test. Population structure was assessed in terms of proportion of seedlings, saplings, and trees. Regeneration was analyzed using graphical representation of frequencies of seedlings, saplings, and trees in histograms. Results: The results showed that the population structure of Larix in terms of the proportion of seedling, sapling, and tree varied greatly in the three study areas. KCA had the highest record of seedling, sapling, and tree compared to other two sites. Seedlings were the least among three forms and many plots were without seedlings. We found no seedling in MCA study plots. The plot level average DBH variation among sites was significant (Kruskal-Wallis χ2 = 7.813, df = 2, p = 0.02) as was between species (Kruskal-Wallis χ2 = 5.9829, df = 1, p = 0.014). Similarly, the variation in average tree height was significant (Kruskal-Wallis χ2 = 134.23, df = 2, p < 0.001) among sites as well as between species (Kruskal-Wallis χ2 = 128.01, df = 1, p < 0.001). All the sites showed reverse J-shaped curve but more pronounced for KCA and MCA. In comparing the two species, Larix griffithiana has clear reverse J-shaped diameter distribution but not Larix himalaica. Conclusion: The varied responses of Larix manifested through regeneration status from spatially distinct areas show that regeneration limitations might be more pronounced in the future. In all the three studied valleys, regeneration of Larix is found to be problematic and specifically for Larix griffithiana in MCA and Larix himalaica in LNP. To address the issues of disturbances, especially serious in LNP, management interventions are recommended to sustain the unique Himalayan endemic conifer.