Increasing milk production requires increasing milking frequency (MF) from two times daily (2X) to three (3X) or more. High milk production leads to negative energy balance (NEB) and homeorhesis, characterized by lipolysis, ketogenesis, and endocrinological changes. The relationship among energy balance (EB), lipolysis, and ketogenesis with endocrine and metabolic parameters in blood of cows milked 2X and 3X daily was studied. Holstein Friesian cows milked 2X (n = 45) and 3X (n = 45) were analyzed, with approximately 50% of cows in each group in positive EB (PEB) and 50% in NEB. After determining EB, blood samples were collected from all cows and blood serum was analyzed for non-esterified fatty acids (NEFA), beta-hydroxybutyrate (BHB), glucose (GLU), cholesterol (CHOL), triglycerides (TGC), total bilirubin (TBIL), aspartate aminotransferase (AST), gamma-glutamyl transferase (GGT), calcium (Ca), inorganic phosphate (P), total protein (TPROT), albumin (ALB), urea, insulin (INS), T3, T4, and cortisol (CORT), and the RQUICKIBHB index of insulin resistance was calculated. Cows milked 3X in NEB represent a special cluster that partially overlaps with cows milked 2X in NEB and has no contact points with cows in PEB. Cows milked 3X had higher levels of NEFA, BHB, AST, GGT, TBIL, and CORT and lower levels of GLU, Ca, INS, and T4. Cows milked 3X in NEB had higher levels of NEFA, BHB, AST, GGT, TBIL, and CORT and lower levels of GLU, CHOL, TGC, TPROT, P, INS, RQUICKIBHB, and T3 compared with cows milked 2X in NEB and cows in PEB. In cows milked 3X, lipolysis and ketogenesis were much more prominent, and EB levels were lower, implying a pronounced shift in homeorhesis. Metabolic and endocrinology parameters were determined mainly by the values of EB, NEFA, and BHB in cows milked 3X in NEB compared with other categories of cows. The results confirm the peculiarity of metabolic adaptation in cows with increased MF, characterized not only by differences in the concentration of metabolites but also in their interactions.