We aimed to assess liver histological changes of HBeAg-negative chronic hepatitis B (CHB) patients with normal ALT, and determined the association between significant liver injury and age, ALT, and HBV DNA levels. We retrospectively examined 327 patients who underwent liver biopsy from 2009 to 2018. Significant liver histological change is defined as liver necroinflammation ≥ G2 and/or liver fibrosis ≥ F2. The proportion of patients with significant liver necroinflammation or fibrosis in the high-normal ALT group (ALT > 20 U/L) was higher than that in the low-normal ALT group (ALT ≤ 20 U/L) (44.6% vs 26.5%, 61.0% vs 41.7%, p < 0.01); also the proportion in the group with HBV DNA ≥ 2000 IU/mL was significantly higher than that in the group with HBV DNA < 2000 IU/mL (58.5% vs 27.1%, 67.9% vs 46.2%, p < 0.01). There was no significant difference in hepatic histopathology between < 40 and ≥ 40 years groups. Among 221 patients with normal ALT and low HBV DNA levels (< 2000 IU/mL), 27.1% of them had significant liver necroinflammation and 46.2% had significant liver fibrosis. The multiple logistic regression analysis showed that ALT > 20 U/L and HBV DNA ≥ 2000 IU/mL were independently associated with significant liver histopathology (p < 0.01). HBeAg-negative CHB patients with normal ALT and low HBV DNA level (< 2000 IU/mL) were suggested to perform liver biopsy or noninvasive methods for histopathology assessment, then to be determined for antiviral therapy. ALT > 20 U/L and HBV DNA ≥ 2000 IU/mL are good independently predictive factors for evaluating significant liver histopathology for HBeAg-negative CHB patients with normal ALT. Chinese Clinical Trial Registry (ChiCTR-IOR-14005474).