The aim of this research is to examine the influence of heat stress (HS) on body temperature (BT) measured rectally (RT) or by infrared thermography (IRT) of the nose (NT), eye (ET), leg (LT) and abdominal (AT) regions in intensively and extensively breed sheep and to detect a correlation between body temperature and metabolic response in sheep. A total of 33 Wurttemberg × Sjenica Pramenka sheep breeds were examined, 17 ewes were from outdoors and 16 were from indoor housing systems during three experimental periods (thermoneutral period, severe HS and moderate HS). Sheep under HS have a higher BT, and the magnitude of BT measured by infrared thermography (IRT) was higher than RT. LT and AT showed positive linear correlations with the temperature–humidity index (THI), while other ways of measuring BT did not give statistically significant correlations. Sheep under HS showed higher cortisol, insulin, total protein, albumin, urea, creatinine, bilirubin, aspartate aminotransferase, alanine aminotransferase, gamma-glutamyl transferase, alkaline phosphatase, lactate dehydrogenase, creatine kinase and index of insulin resistance, with lower values of triiodothyronine (T3), thyroxine (T4), non-esterified fatty acids, beta-hydroxybutyrate (BHB), glucose, calcium, inorganic phosphates, magnesium and cholesterol. BT and metabolic response were different in the function of the housing method of sheep. LT and AT showed a significant correlation with almost all blood parameters, and the strongest connections were made with T3, T4, BHB and the revised quantitative insulin sensitivity check index of insulin resistance. The abdomen and legs are good thermal windows because LT and AT are good summative responses to external ambient THI and internal metabolic changes in sheep under heat stress.