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Abstract Background Thrombocytopenia is increasingly prevalent in middle-aged and older individuals. The hemoglobin glycation index (HGI) is related to the prognosis of multiple diseases. However, no studies have assessed the relationship between HGI and platelets (PLT). Utilizing data from the China Health and Retirement Longitudinal Study (CHARLS), this research aimed to examine the associations between HGI, PLT count, and thrombocytopenia. Methods Data were obtained from the 2015 wave of the CHARLS. The association between HGI and PLT count was examined by linear regression models, and the relationship between HGI and thrombocytopenia was investigated using logistic regression models. Subgroup analyses by residence, sex, alcohol consumption, age, smoking, marital status, employment, hyperlipidemia (HLD), hypertension, liver disease, and cardiovascular disease were carried out to examine potential interactions. Results In total, 10,322 participants were included. Restricted cubic spline analysis showed a non-linear relationship between HGI and the prevalence of thrombocytopenia ( P overall = 0.02, P nonlinear = 0.04). After adjusting for covariates, the β value in the Q3 group was 8.50 × 10⁹/L compared to the Q1 group [(95% CI 2.42–14.59), P = 0.006]. When PLT count < 100 × 10⁹/L was used as the threshold for diagnosing thrombocytopenia, the odds ratio (OR) for the Q2 group compared to the Q1 group was 0.64 [(95% CI 0.46–0.89), P = 0.007] in Model 3. When PLT count < 150 × 10⁹/L was used as the threshold, the OR for the Q4 group compared to the Q1 group was 0.77 [(95% CI 0.62–0.97), P = 0.025] in Model 3. Among individuals aged > 60 years in Q2, Q3, and Q4, higher HGI was associated with a lower prevalence of thrombocytopenia. In female participants, elevated HGI (Q2 and Q4) was associated with a decreased prevalence of thrombocytopenia. Among individuals without HLD, elevated HGI (Q2) was associated with a decreased prevalence of thrombocytopenia. Furthermore, increased HGI (Q3 and Q4) was positively associated with PLT count in the following subgroups: female participants, rural residents, and those without HLD. Conclusion There is a non-linear relationship between HGI and thrombocytopenia. Moderately high HGI is associated with a lower prevalence of thrombocytopenia.