Hibernation, a natural physiological state characterized by reduced energy expenditure, represents a survival strategy adopted by organisms to endure adverse environmental conditions such as low temperatures and food scarcity. Amphibians frequently endure harsh hibernation conditions characterized by low temperatures and hypoxia, yet they typically exhibit rapid physiological recovery upon arousal without sustaining permanent organ or tissue damage. These remarkable capabilities stem from specialized organ-protective mechanisms and adaptive physiological regulation unique to hibernating species. This study employed Data-Independent Acquisition (DIA) quantitative proteomics technology to conduct comprehensive quantitative proteomic and phosphoproteomic analyses of the kidneys, liver, and lungs in Pelophylax nigromaculatus during hibernation, followed by multi-dimensional analysis of the protein regulatory strategies. Our multidimensional analytical approach elucidated intricate protein regulatory strategies underlying this hypometabolic state. The findings provide substantial and reliable datasets for advancing molecular investigations into hibernation mechanisms in amphibians, while establishing a foundational framework for understanding the molecular regulation of low-energy metabolism in animals.