Juglans cathayensis is an endangered plant species and listed as a class II protected species of the national government of China. In order to grasp the current state of J. cathayensis populations and predict the population dynamics in the future, a large-sample investigation was conducted in the sample plots along different altitude gradients in four valleys in J. cathayensis conservation area. According to the diameter at breast height (DBH) class of the trees, the age class structures of the populations were analyzed, and static life tables for J. cathayensis populations in different habitats along the altitude gradient was constructed by smoothing out technique, and comparative fluctuations cycles of the populations in different habitats were carried out by spectral analysis. The results showed that DBH decreased gradually with the increasing altitude. The population was composed of 19 age classes in the low-altitude habitat (1241 - 1380 m) with the maximum DBH of 91.7 cm, 18 age classes in the middle-altitude habitat (1381 - 1490 m) with the maximum DBH of 82.8 cm, and 13 age classes in the high-altitude habitat (1491 - 1670 m) with the maximum DBH of 58.9 cm. Life expectancies of J. cathayensis populations were fluctuant for the same age class at different altitudes and for different age classes at the same altitude. In the three altitude-different habitats, the survival curves of the populations trended toward Deevey- II type and the age structures of the populations were expanding. The curves of mortality showed three peaks, and the mortality rates of 9 age classes at 1241 - 1380 m and 1491 - 1670 m above sea levels were the highest, being 55.9% and 89.8%, respectively, and the mortality rate of 12 age classes at 1381 - 1490 m above sea level was the highest (79.4%). The population dynamics was significantly affected by the fundamental wave of biological characteristic throughout the life cycle of J. cathayensis population, and small cycles of multi-harmonic superposition with large cycles were presented. J. cathayensis is a long lifespan tree and a major dominant species in this conservation area. The natural regeneration of its current populations is good. If not strong anthropogenic disturbances or severe natural disasters, J. cathayensis would maintain the dominant position in the community.