<p>Periodontal ligament stem cells (PDLSCs) are regarded as among the most promising seed cells for periodontal tissue regeneration because of their strong self-renewal ability, multipotent differentiation potential, and accessibility. However, their biological behaviors vary significantly under different microenvironments and stimuli, and the underlying regulatory mechanisms remain unclear. Recent advances have identified mitochondria as central signaling hubs that regulate cell fate. This review summarizes current progress in understanding the role of mitochondria in modulating the biological behaviors of PDLSCs, focusing on mitochondrial reactive oxygen species and oxidative stress, mitochondrial dynamics, mitophagy, glucose metabolic reprogramming, and tricarboxylic acid cycle metabolites. We integrate evidence linking mitochondrial function with key biological processes in PDLSCs, including osteogenic differentiation, senescence, inflammation, apoptosis, and regenerative capacity. Furthermore, we highlight major unresolved issues and challenges in current research and emphasize the significant “dual effects” of mitochondria-related signaling in diverse physiological and pathological conditions. A deeper understanding of mitochondrial regulatory networks in PDLSCs may provide a theoretical foundation for mitochondria-targeted precision therapies and reveal novel therapeutic strategies for periodontal tissue regeneration and related diseases.</p>