The development of ways to increase the adaptive reserves of the body and resistance to negative factors continues to be an urgent problem for physiology, which has a significant translational potential in the fields of healthcare, sports, cosmonautics and the national economy. Long-term authors studies have proved the promise in this respect of hypoxic hypobaric conditioning in a pressure chamber. In the present study, the principles of hypobaric conditioning were transferred to the model of normobaric intermittent hypoxia/normoxia caused by the inhalation of gas mixtures, which is widely used in practice for human interval hypoxic training. A comparative experimental analysis of molecular and cellular changes in the blood of rats in response to three-day interval hypoxic training at 9, 12, or 16% O2 in the mixture was carried out using an automated setup. It was shown that the most intense and effective 3 × 9% O2 regimen, in terms of duration and amplitude, had the greatest effect on the parameters of the clinical blood test of rats, initiating an increase in the number of erythrocytes and a decrease in the variability of their volumes, and causing a shift in the balance of lymphokine and monokine effects towards a calm activation reaction. On the first day after training at 9 and 12% oxygen, the total antioxidant capacity of serum significantly decreased, followed by rapid normalization, which fits into the dynamics of the reaction of pro- and antioxidant systems to non-damaging hypoxia. The stimulating effect of all the studied regimens of interval training on the basal and stress activity of the hypothalamic-pituitary-adrenocortical system, characteristic of conditioning, was revealed. All detected post-training changes can be attributed to the basic adaptive mechanisms that increase resistance to adverse factors.