Abstract: Over the past two decades, advances in high-throughput-sequencing technology platforms and in the recovery of highly degraded DNA have ushered ancient DNA research into the era of deep-time paleogenomics, expanding sample ages from no more than 100 ka to the Early Pleistocene (~2 Ma). These developments have resolved long-standing phylogenetic controversies, refined reconstructions of the dispersal and population history across diverse taxa (including humans), and enabled direct investigation of molecular response to Quaternary climate change. Paleogenomics in China developed later than in Europe and North America, with early landmark breakthroughs largely focused on ancient human remains. However, China preserves one of the richest and most distinctive records of Quaternary megafauna, many lineages of which are morphologically and genetically differentiated from their western Eurasian counterparts. Here, we synthesize recent paleogenomic advances across major megafauna clades, including Proboscidea, Perissodactyla, Artiodactyla, and large Carnivora, to evaluate how time-resolved genomic data are reshaping systematics, phylogeography, and evolutionary interpretation of the Chinese Quaternary fauna. Current megafauna paleogenomic coverage remains taxonomically and geographically biased toward northern assemblages and mitochondrial datasets. We therefore outline key methodological and sampling priorities, including coordinated recovery of nuclear genomes and improved approaches for southern contexts with poor preservation, to position Chinese megafaunal paleogenomics as a platform for testing general models of megafauna responses to Quaternary climatic oscillations. These efforts refine the systematics and evolutionary history of Chinese Quaternary megafauna and provide a conceptual model for understanding how megafauna respond to Quaternary climate oscillations worldwide.

Key words: faunal turnover, gene flow, paleogenomics, phylogenetics, phylogeography, Quaternary megafauna