Despite the endangered status of the Oriental Stork (Ciconia boyciana) on the IUCN Red List, a critical lack of contemporary mitochondrial genomic data from its core distribution areas in mainland China has hindered our understanding of the species’ long-term evolutionary stability and spatiotemporal variation. This study addresses this gap by sequencing and assembling the complete mitogenome (17,608 bp) of a contemporary individual from Hongze Lake, Jiangsu (PX682155), and conducting a rigorous comparative analysis against a historical reference sequence published 25 years ago in Japan (NC_002196). Our results demonstrate striking structural and functional conservation across a quarter-century span; the 13 protein-coding genes exhibit highly synchronized gene arrangements, base composition biases, and Relative Synonymous Codon Usage (RSCU) patterns, indicative of stringent purifying selection maintaining oxidative phosphorylation efficiency. While phylogenetic analysis reinforces its sister-group relationship with the White Stork (C. ciconia), significant length polymorphisms were identified within the D-loop control region, primarily driven by microsatellite repeat variations. These findings provide a vital genomic benchmark for mainland populations, offering high-resolution molecular markers essential for future large-scale assessments of geographic isolation and the refinement of targeted conservation strategies for this flagship wetland species.