Hibernation is a low-energy consumption survival strategy adopted by organisms to cope with adverse environments such as low temperatures and food scarcity. This study used the Pelophylax nigromaculatus as the model organism, and for the first time comprehensively analyzed the proteomic and phosphoproteomic regulatory networks in its kidneys, liver, and lungs through DIA quantitative proteomics technology, revealing specialized organ protection mechanisms under the hypometabolic state of hibernation. The research found that the regulation of these proteins relates to glycolysis and glycogenolysis, enhanced intracellular substance transport, membrane repair and energy buffering, rapid degradation of glycation end products, mitigation of inflammatory responses, and maintenance of signal transduction and cellular morphology. Using the glycogenolysis inhibitor CP-91149 to block glycogen breakdown, the study investigated frog hibernation status when glycogenolysis was inhibited to a certain extent, with results showing these frogs exhibited higher mortality during hibernation. This research not only provides substantial reliable data for elucidating the molecular mechanisms of amphibian hibernation but also establishes a foundational framework for understanding the molecular regulation of animal low-energy metabolism.