The study of the effect of environmental factors and the possibilities of correcting their influence, especially during war, cannot occur without taking into account changes in the organism’s energy metabolism. Recently, intermittent hypoxic training (IHT) has been used extensively for altitude preacclimatization, for the treatment of a variety of clinical disorders, and in sports. Amaranth oil has an antioxidant, membrane-protective effect. Therefore, it is possible to apply it to maintain the structural and functional integrity of cellular and subcellular membranes during fluoride intoxication. The aim of the present study was to evaluate changes in morphologic characteristics of liver tissues and the state of energy metabolism in rats with chronic fluorine intoxication treated by intermittent hypoxic training and with an amaranth oil feeding supplement. Fluorine intoxication was induced by oral administration of sodium fluoride (10 mg/ kg) for 30 days. IHT was carried out in a pressure chamber as follows: five 10-min elevations to the “height” of 3000 m were repeated 5 times with 15-minute intervals for 10 days. At the same time, rats were fed amaranth oil in the diet at a daily dose of 38 mg/kg for 10 days. The liver tissue specimens underwent electron microscopy examination. It was found that both intermittent hypoxic training and amaranth oil contributed to the normalization of energy metabolism and liver ultrastructure under chronic fluoride intoxication. The ultrastructural organization of sinusoidal hemocapillaries, biliary hemocapillaries and the cytoplasm of hepatocytes indicates a powerful corrective effect of both amaranth oil and IHT in fluoride intoxication. The simultaneous application of IHT and amaranth oil with chronic exposure to fluorides leads to the normalization of energy metabolism and, as a result, to the complete restoration of the structure of organ elements due to the sufficient strengthening of intracellular reparative regeneration. The high efficiency of the combined application of IHT and amaranth oil against damage to the structure and function of organs and cells, proven based on biochemical indicators and ultrastructural characteristics, justifies the expediency of including these factors in the complex correction of metabolic processes under fluoride intoxication.