Emerging epidemiological evidence indicates that low serum high-density lipoprotein cholesterol (HDL-C) levels are associated with the risk of progression of chronic kidney disease (CKD). However, the differences in the influence of serum HDL-C levels on CKD progression in different subcohorts have rarely been examined in detail in previous studies. The aim of this study was to investigate the significance of low serum HDL-C levels as a predictor of disease progression in CKD patients according to sub-analyses using a cross-classified subcohort. We reviewed data obtained from 120 CKD patients. Prognostic factors for renal outcome were identified by the multivariate Cox proportional hazards method. Kaplan-Meier analysis was performed to assess disease progression, which was defined as a > 30% decline in the glomerular filtration rate (GFR), or end-stage renal disease. The mean age of the included participants was 58.3 ± 13.6 years. The subjects were divided into two groups (low HDL-C vs. high HDL-C). The median follow-up period was 112.8 months. The kidney survival rate in the low HDL-C group was significantly lower than that in the high HDL-C group (P < 0.0001). However, the age-stratified analysis showed no difference between the two groups in the cohort of patients ≥ 70 years old. Multivariate Cox regression analyses showed a significant association between low HDL-C [hazard ratio (HR) 4.80, P = 0.009] and a ≥ 30% eGFR decline or ESRD. This association was more evident in the cohort of patients < 70 years old (HR 4.96, P = 0.0165), especially the female subcohort (HR 13.86, P = 0.0033). Multivariate analysis showed a significant correlation between visceral fat area and serum HDL-C levels among both male (P = 0.0017) and female (P = 0.0449) patients. In a propensity score-matched cohort (patients < 70 years old), the kidney survival rate of CKD patients was significantly lower in the low HDL-C group than in the high HDL-C group (P = 0.0364). A low serum HDL-C level is a significant predictor of CKD progression, especially in female patients with CKD under 70 years of age. This finding is of importance to clinicians when determining the expected prognosis of CKD in patients.