Objectives: The objective of this study was to examine the association between non-high-density lipoprotein cholesterol (non-HDL-C) to high-density lipoprotein cholesterol (HDL-C) ratio (NHHR) and chronic kidney disease (CKD) in Chinese adults with type 2 diabetes mellitus (T2DM). Methods: This study originated from a survey carried out in Zhejiang Province, located in eastern China, between March and November 2018. To explore the relationship between NHHR and CKD, a multivariable logistic regression model was employed. The dose–response relationship was assessed using restricted cubic spline (RCS) analysis, while generalized additive models (GAMs) were applied to examine the associations between NHHR and urinary albumin-to-creatinine ratio (UACR) as well as estimated glomerular filtration rate (eGFR). Subgroup analyses were performed across various demographic and clinical categories to assess the consistency of the NHHR–CKD association. The optimal NHHR cutoff for CKD diagnosis, its predictive accuracy, and its comparison with its components and HbA1c were determined through receiver operating characteristic (ROC) curve analysis. Results: The study enrolled 1756 participants, including 485 individuals with CKD and 1271 without CKD. Multivariable logistic regression revealed a significant positive association between NHHR and CKD, with each standard deviation (SD) increase in NHHR linked to a 23% higher odds of CKD (OR = 1.23, 95% CI: 1.09–1.37) after adjusting for potential confounders. When comparing quartiles, the fully adjusted ORs for Q2, Q3, and Q4 were 1.29 (0.92–1.79), 1.31 (0.94–1.83), and 1.87 (1.34–2.60), respectively, relative to Q1 (p for trend < 0.01). RCS analysis confirmed a linear dose–response relationship between NHHR and CKD in both sexes (p for nonlinearity > 0.05). GAMs indicated a significant positive correlation between NHHR and UACR (ρ = 0.109, p < 0.001) but no significant association with eGFR (ρ = −0.016, p = 0.502). Subgroup analyses demonstrated consistent associations across most subgroups, except for the 18–44 years age group, the well-controlled glycemic group, and the non-alcohol drinking group (p > 0.05). ROC curve analysis identified an optimal NHHR cutoff of 3.48 for CKD prediction, with an area under the curve (AUC) of 0.606 (95% CI: 0.577–0.635). Notably, NHHR outperformed its individual components and HbA1c in predictive performance. Conclusions: This study revealed a linear link between higher NHHR levels and increased CKD prevalence in Chinese T2DM patients. NHHR may also serve as a potential complementary biomarker for early CKD detection, though further prospective studies are needed to confirm its predictive value and clinical utility in high-risk T2DM populations.