Species conservation, especially of endangered species, has become a major focus of the international ecology community. Global biodiversity is in decline, which is affecting ecosystem functioning, and efforts to protect and mitigate this decline are necessary. Within the last few years, the endangered plant species Abies chensiensis has experienced unexplained mortality in the Xiaoqinling national nature reserve. The analysis of potential causes of this mortality is necessary to avoid further loss of A. chensiensis. This study examines the condition of living trees to identify the cause of this widespread mortality and suggests a management plan for the protection and population recovery of A. chensiensis. Ecological communities are complex systems characterized by multiple interacting processes, and the growth and death of species is a complex process. Univariate statistical methods do not provide sufficient information to identify the requirements of ecological development. The structural equation model (SEM) is a multivariate statistical method that can solve complex problems and that is increasingly applied by ecologists to solve complex problems. SEMs provide a unique perspective in addressing scientific questions. A census of all living and dead A. chensiensis trees in Xiaoqinling was used for a comparative analysis. The distribution pattern and structure of living and dead trees, combined with correlation analysis, partial correlation analysis, and SEM was used to explore the conditions of live individuals and the cause of mortality. Dead trees had similar distribution patterns as living trees. The ratio of large and small trees was small for living A. chensiensis; dead trees were mostly young and middle-aged individuals. The distribution of A. chensiensis was significantly correlated with elevation, slope, soil moisture, and soil temperature. SEM analysis showed that the living individuals were significantly positively correlated with soil heterogeneity, while dead trees showed a negative correlation. There was a stronger negative correlation between dead trees and position and topography compared to living trees. These results suggest that the numbers of A. chensiensis seedlings and young trees are low and that the ability of the species to regenerate is poor. Abies chensiensis mortality is likely caused by local environmental changes, rather than by a single phenomenon, and the growth and regeneration of A. chensiensis is closely related to elevation, slope, and soil water content. To protect A. chensiensis, changes in the microenvironment must be minimized and human interference with the environment must be reduced. Heterogeneity of soil moisture and temperature promotes growth and is an important environmental factor that influences mortality. The observed mortality of A. chensiensis may be a result of human activity and gradual climate change that has affected precipitation, temperature, and other environmental factors.