Trunk internal decay in live standing trees threatens forest health, stability, and sustainable management in forest ecosystems. Populus euphratica Oliv. is a unique non-zonal forest vegetation species in desert riparian forests of extremely arid regions. Approximately 54 % of the world's natural P. euphratica forests are distributed in the Tarim River Basin in China. However, these forests exhibit widespread trunk decay, and the mechanisms of trunk decay under the influence of multiple stresses and the tree's intrinsic characteristics remain unclear. This study focuses on natural P. euphratica riparian forests in the lower reaches of the Tarim River, employing nondestructive stress wave detection technique and high-throughput sequencing technology to explore the characteristics and driving mechanisms of trunk decay in P. euphratica, and to develop conservation strategies. The major research findings were as follows: 1) Trunk decay of P. euphratica predominantly occurs in older and low-vitality individuals. The decay proportion of P. euphratica with a diameter at breast height (DBH) more than 40 cm ranges from 21.56 % to 59.31 % across different moisture gradients. 2) The random forest (RF) models combined with the Shapley Additive Explanations (SHAP) method demonstrated robust explanatory power and strong predictive accuracy in quantifying the key drivers of trunk decay (R2 = 0.926-0.951; RMSE = 1.673-2.064). Low tree vitality and aging individuals, along with poor nutrients and limited moisture availability are more likely to facilitate trunk decay in P. euphratica. 3) The differences in microbial community structure were important factors leading to trunk decay. Severely decayed samples showed enrichment of microbial species mainly concentrated in P_Euryarchaeota, P_Basidiomycota, G_Actinotalea, G_Methanobacterium, G_Cortinarius, G_Pseudallescheria, G_Fusicolla, G_Paracremonium and G_Microascus at the phylum and genus levels. Based on these findings, sustainable forest management strategies were proposed, including dynamic health monitoring, optimized water allocation, soil nutrient enhancement, and eco-friendly microbial control measures. By addressing the driving factors, this study supports the conservation of P. euphratica forests and provides a framework for managing desert riparian ecosystems globally, enhancing forest resilience and ecological stability in arid regions under increasing environmental stress.