In this study, we aim to investigate associations between body fat parameters, glucose and lipid profiles, thyroid-stimulating hormone (TSH), and thyroid hormones (THs) levels in Tomsk-region schizophrenia patients depending upon the presence or absence of metabolic syndrome (MetS). A total of 156 psychiatric inpatients with schizophrenia who had been treated with antipsychotics for at least six months before entry were studied: 56 with and 100 without MetS. Reference groups consisted of general hospital inpatients with MetS and without schizophrenia (n = 35) and healthy individuals (n = 35). Statistical analyses were performed using the Mann–Whitney U-test, chi-square test, Spearman’s rank correlation coefficient, multiple regression analyses, and descriptive statistics. Patients with schizophrenia and MetS had significantly higher levels of free triiodothyronine (FT3) and thyroxine (FT4) compared to schizophrenia patients without MetS (3.68 [3.25; 5.50] vs. 3.24 [2.81; 3.66], p = 0.0001, and 12.68 [10.73; 15.54] vs. 10.81 [9.76; 12.3], p = 0.0001, in pmol/L, respectively). FT3 maintained an association with MetS (p = 0.0001), sex (p = 0.0001), age (p = 0.022), and high-density lipoproteins (p = 0.033). FT4 maintained an association with MetS (p = 0.0001), sex (p = 0.001), age (p = 0.014), and glucose (p = 0.009). The data obtained showed body fat parameters, glucose and lipid profiles, and THs levels in Western-Siberian schizophrenia patients depending on MetS presence or absence.