To investigate the pathological characteristics and pathogenesis of visceral white spot disease in Hapalogenys mucronatus, anatomical observations, tissue sectioning, and ultra-thin section electron microscopy were used to conduct a pathological analysis of the thymus, spleen, gills, liver, kidneys, intestines, and ovaries of affected fish. The results showed that clinical symptoms in H. mucronatus included ulceration and hemorrhage on the body surface, ulceration and bleeding at the base of the pectoral, caudal, and dorsal fins, visible whitish nodules in the gills, thickening and severe fibrosis of the ovarian membrane in females, and numerous white nodules in visceral organs such as the spleen, liver, and kidneys. Histopathological examination revealed that the spleen, thymus, liver, and kidneys were the main target organs for infection and injury, showing severe tissue degeneration and necrosis with pronounced vacuolation. Pathological nodules were observed in all the affected tissues. Ultrastructural pathology results showed severe damage to the cellular ultrastructure of the spleen, thymus, liver, and kidneys of the affected fish, particularly mitochondrial and nuclear damage. Mitochondrial swelling, cristae disruption, and vacuolization were observed, along with nuclear shrinkage, chromatin marginalization, and clustering of numerous pathogenic bacteria. The results indicate that tissue cellular pathology and ultrastructural pathological characteristics of visceral white spot disease in H. mucronatus demonstrate the invasion and harm caused by pathogenic bacteria, primarily resulting in damage to respiratory-, immune-, and reproductive-related tissue organs, ultimately leading to death, while potentially exerting a negative impact on reproductive capacity.