Background & Aims: Hepatitis B virus (HBV) can be completely suppressed after antiviral treatment; however, some patients with chronic hepatitis B (CHB) still exhibit elevated alanine aminotransferase (ALT) levels and sustained disease progression. The aim of this study was to provide novel insights into the mechanism and potential predictive biomarkers of persistently elevated ALT (PeALT) in patients with CHB after complete viral inhibition. Methods: CHB Patients with undetectable HBV DNA at least 12 months after antiviral treatment were enrolled from a prospective, observational cohort. Correlations between plasma metabolites and the risk of elevated ALT were examined using multivariate logistic regression. Results: Of the 1238 patients with CHB who achieved complete viral suppression, 40 (3.23%) had PeALT levels during follow-up (median follow-up: 2.42 years). Additionally, 40 patients with persistently normal ALT (PnALT) levels were matched 1:1 as controls. Ser-Phe-Ala (variable importance in projection [VIP] = 4.28), Lys-Ala-Leu-Glu (VIP = 4.49), 3-methylhippuric acid (VIP = 3.04), 3-methylxanthine (VIP = 2.62), and 7-methylxanthine (VIP = 3.35) were identified as critical differential metabolites between the two groups and independently associated with PeALT risk. Ser-Phe-Ala and Lys-Ala-Leu-Glu levels could be used to discriminate patients with PeALT from those with PnALT. Furthermore, N-acetyl-l-methionine (NALM) demonstrated the strongest negative correlation with ALT levels. NALM supplementation alleviated liver injury and hepatic necrosis induced by carbon tetrachloride in mice. Conclusions: Changes in circulating metabolites may contribute to PeALT levels in patients with CHB who have achieved complete viral suppression after antiviral treatment.