Impaired fasting glucose (IFG) is a reversible intermediate hyperglycemia stage with an increasing risk of diabetes and related complications. Our study was designed to identify the relationship between the serum anion gap and the risk of progressing to impaired fasting glucose and diabetes. Here, we performed a prospective, population-based study among 1191 Chinese individuals aged 22-87 years who took health examinations annually between 2006 and 2012 including clinical features and plasma metabolites. All of the participants had no history of diabetes or related chronic complications. Logistic regression analysis was designed to examine the associations between clinical and metabolomic factors and the risk of developing IFG or diabetes. Among them, 58 subjects whose fasting glucose were between 6.1 and 7 mmol/L were diagnosed as IFG or diabetes. After adjusting for age, sex, body mass index (BMI), high-density lipoprotein (HDL), low-density lipoprotein (LDL), alanine aminotransferase (ALT), aspartate aminotransferase (AST), systolic blood pressure (SBP), diastolic blood pressure (DBP), potassium, and albumin at baseline, the participants in the upper tertiles of serum anion gap (SAG) had higher odds of progressing to IFG or diabetes than those in the lower tertiles. A receiver operating characteristic (ROC) curve was analyzed, and the optimal cutoff level for the anion gap to predict incident IFG or diabetes was 13.76 mmol/L, and the area under the ROC curve (AUC) was 0.623. Our data demonstrate that a higher serum anion gap is associated with the risk of developing IFG or diabetes.