To explore the relationship between glucose management indicator (GMI) and HbA1c and find the affecting factors in adult T2D patients with good glycemic control. Adult T2D patients with both HbA1c < 7% and time in range (TIR) > 70% were retrospectively analyzed. A significant difference between GMI and HbA1c was defined as an absolute value of hemoglobin glycation index (|HGI|, HbA1c minus GMI) ≥ 0.5%. Factors associated with high |HGI| were determined by logistic regression analysis. The performance of possible factors in predicting high |HGI| was verified by ROC curve analysis. And the linear relationship between GMI and HbA1c was also investigated. Of all the 94 patients (median HbA1c 6.18%, mean GMI 6.34%) included, 28.72% had an |HGI | ≥ 0.5% and only 15.96% had an |HGI | < 0.1%. Standard deviation of blood glucose (SDBG), a glycemic variability index, affected |HGI| (OR = 3.980, P = 0.001), and showed the best performance in predicting high |HGI| (AUC = 0.712, cutoff value = 1.63 mmol/L, P = 0.001). HbA1c was linearly correlated with GMI (β = 0.295, P = 0.004). Their correlation weakened after further adjusting for SDBG (β = 0.232, P = 0.012). Linear correlation between them was closer in patients with smaller SDBG ( < 1.63 mmol/L) than those with larger SDBG (P = 0.004). Even in adult T2D patients with good glycemic control, the discrepancy between GMI and HbA1c existed. Their relationship was affected by glycemic variability. SDBG mainly accounted for this consequence. Chinese clinical trial registry ( www.chictr.org.cn ), ChiCTR2000034884, 2020-07-23.