Purpose: To explore the association between the anti-inflammatory and renal protective roles of high-density lipoprotein cholesterol (HDL-c) and its different levels in type 2 diabetes mellitus (T2D), hypertension (HTN), and chronic kidney disease (CKD) and to lay a theoretical basis for precise, maximum-benefit HDL-c-raising therapy for patients with these diseases. Patients and Methods: A total of 2127 participants (195 with T2D, 618 with HTN, 162 with CKD, and 1152 controls) were selected and divided into four groups according to their baseline HDL-c level, namely, low HDL-c (L-HDL-c, ≤1.03 mmol/L), medium HDL-c (M-HDL-c, 1.04-1.55 mmol/L), high HDL-c (H-HDL-c, 1.56-2.05 mmol/L) and extremely high HDL-c (E-HDL-c, ≥ 2.06 mmol/L). Serum and morning urine samples were collected to analyze the correlation between high-sensitivity C-reactive protein (HsCRP), interleukin-6 (IL-6), urine n-acetyl-β-d-glucosidase (U-NAG), retinol binding protein (RBP), and cystatin c (Cys-C) levels with the HDL-c levels. Results: The HDL-c levels of patients with T2D, HTN and CKD were universally lower than those in the control group in both sexes (p<0.05), while male patients also manifested a lower level of HDL-c than female patients. However, although they had lower values of the renal impairment index, female patients were found to have anomalously higher amounts of proinflammatory cytokines. In addition, the correlations between HsCRP and RBP levels and HDL-c levels were most significant in patients with HTN (p<0.05), whereas in patients with T2D and CKD, such relevance was less significant. Conclusion: Existence of substantial differences in HDL-c levels between different types of disease and sex highlighted that a higher HDL level does not always predict a better clinical outcome of patients. Moreover, we found that both HsCRP and RBP correlated negatively with HDL-c in HTN patients, indicating that monitoring HsCRP and RBP may serve as indicators for therapeutic efficacy of HDL-c-raising medications in HTN patients.