The use of organic compounds of iodine, selenium, and sulfur is limited due to the complexity of their chemical synthesis. The latest nanotechnological methods of obtaining organic compounds I, Se, S provide the opportunity to replace their mineral and organic salts with citrate mixtures synthesized on the basis of nanotechnology. This provides a perspective for the use of nanocomposition citrates I, Se, S in biology, medicine and animal husbandry. The research aimed to determine the effect of different doses of I, Se, S nanoparticles citrates on the activity of the pituitary-thyroid system and metabolism in the blood of male rats. The animals of the experimental groups received daily with water a mixture of I, Se, S in experimentally determined ratios (3:1:5) by mass of elements and doses, according to the concentration of iodine in μg/kg of body weight: 1–2.4 (low); 2–24 (average); 3–240 (high); 4–2400 (toxic). Blood for laboratory studies was taken on the 40th day of drinking I, Se, S after the decapitation of animals. The content of thyroid-stimulating hormone (TSH), triiodothyronine (T3), thyroxine (T4), thyroglobulin (Tg), antibodies to thyroglobulin (Anti-Tg) and thyroperoxidase (Anti-TPO), as well as hematological and biochemical indicators characterizing the activity of physiological systems of the body, were determined in the blood. Activation of the body’s immune system was established with an increase in the number of monocytes in the blood of rats of the experimental groups under the influence of all applied doses of I, Se, S, and platelets – only in doses of 2.4, 24, and 240 μg of iodine. The effect of the toxic dose led to an increase in the number of leukocytes in the blood of animals of the 4 group, with a decrease in platelets. A probable decrease in the relative level of lymphocytes and an increase in monocytes in the blood of rats in the experimental groups characterized changes in the leukogram of blood. The applied doses of I, Se, S stimulated the synthesis of cholesterol and the influx of calcium into the peripheral blood of rats of the experimental groups. Still, they inhibited the activity of alkaline phosphatase and the creatinine content. The toxic effect of I, Se, S nanoparticles citrates in a dose of 2400 μg of I led to a significant increase in the activity of aminotransferases and a decrease in alkaline phosphatase, phosphorus level, and body weight in rats. The effect of high and toxic doses of I, Se, S nanoparticles citrates on the functioning of the pituitary-thyroid system led to a decrease in the concentration of TSH, T3, T4, and Tg against the background of an increase in Anti-TPO and Anti-Tg in the blood serum of rats of experimental groups.