The prevalence of heatwave and hypoxia events and their devastating impacts on aquatic ecosystems and fishery resources reinforces the priority of research to address the resilience and adaption mechanisms to these two stressors in important fish species. However, our understanding of the development of cross-tolerance of these two stressors in fish still limited. Here, we investigated the impacts of prior heatwave exposure on hypoxia tolerance and the underlying mechanisms in silver carp (Hypophthalmichthys molitrix), a species of considerable ecological and commercial importance. Our results revealed that prior heatwave exposure significantly reduced the dissolved oxygen levels required to induce aquatic surface respiration (ASR50) and loss of equilibrium (LOE50) in juvenile silver carp, indicating the development of cross-tolerance to hypoxia. Physiologically, prior exposure to heatwaves significantly induced gill remodeling by triggering extensive apoptosis. These pre-existing physiological alterations and similar morphological alterations induced by subsequent hypoxia resulted in cumulative effects, leading to extensive gill remodeling under hypoxic conditions and thereby improving hypoxia tolerance. Molecularly, heatwave exposure modulated the expression of critical genes associated with hypoxia adaptation with tissue-specific responses. In the gill, heatwave exposure activated the hypoxia-induced factor (HIF) signaling pathway, increasing oxygen transport (VEGF-A, HB-β) and antioxidant gene expression (GPx, SOD2), facilitating rapid adaptation to hypoxia. In the liver, this exposure resulted in accelerated and enhanced gene expression of HIF-1α, anaerobic metabolism (GLUT-1, LDH-A), and heat shock protein (HSP70) under hypoxic conditions, contributing to improved adaptation. These results highlighted that prior exposure to heatwaves provided cross-tolerance to silver carp, bolstering their resilience to hypoxia through physiological gill remodeling and tissue-specific transcriptional adjustments. Our findings shed light on the intricate interactions of silver carp's thermal and hypoxic stress resilience, offering valuable perspectives for predicting and alleviating climate change impacts on aquatic life.