The diagnostic value of liver biopsy has been confirmed in patients with abnormal liver test results; however, little data are available on its application in patients with portal hypertension. This study aimed to investigate the utility of liver biopsy for the etiological diagnosis of unexplained portal hypertension, and explore the clinical and pathological characteristics of each etiology. A retrospective observational analysis was conducted on 1367 patients who underwent liver biopsy at the Second Hospital of Nanjing from 2017 to 2019. Of these, 188 patients with unexplained portal hypertension were enrolled. The clinical and pathological characteristics were collected and reassessed in a multidisciplinary team meeting. Among these patients, 174 (92.6%, 174/188) had a definite etiological diagnosis through liver biopsy. The main etiologies were autoimmune hepatitis in 47 patients (25%, 47/188), autoimmune hepatitis-primary biliary cirrhosis overlap syndrome in 41 patients (21.8%, 41/188), and porto-sinusoidal vascular disease (PSVD) in 40 patients (21.3%, 40/188). Compared to liver cirrhosis, PSVD patients were younger and the liver function damage of which was subtler. The widths of portal vein diameter were widest in PSVD but the liver stiffness measurement were almost normal. Splenomegaly was common in PSVD, but ascites were less frequent than in autoimmune hepatitis (25.0% vs 51.1%, P = .013). Based on the histological patterns, we found that cholestatic liver diseases such as primary biliary cirrhosis, autoimmune hepatitis-primary biliary cirrhosis overlap syndrome, and progressive familial intrahepatic cholestasis could lead to non-cirrhotic portal hypertension, while vascular liver diseases such as PSVD and Budd-Chiari syndrome could also show fibrous proliferation as the disease progresses. Liver biopsy is safe and valuable for etiological diagnosis of unexplained portal hypertension. Cirrhosis is the leading cause of portal hypertension, and porto-sinusoidal vascular diseases should also be considered. Clinical features may be helpful in suggesting the cause; however, pathological examination is still indispensable for disease diagnosis and progression assessment.