To investigate the characteristics and diagnostic value of three-dimensional contrast-enhanced magnetic resonance angiography (3D CE-MRA) in the diagnosis of Budd-Chiari syndrome (BCS). One hundred thirty-three BCS patients underwent 3D CE-MRA, 64 patients had primary BCS, and 69 had secondary BCS. Fifty five cases (41.4%) showed a segmental stenosis of the inferior vena cava, 9 cases (6.8%) a membranous obstruction of the inferior vena cava, 5 cases (3.8%) an unobstructed inferior vena cava and hepatic veno-occlusive condition, 16 cases (12.0%) an inferior vena cava stenosis and hepatic veno-occlusive disease, and 48 cases (36.1%) an intraluminal filling defect in the inferior vena cava. In 52 cases (39.1%), collateral blood vessels were formed, with deep, medium, and shallow portal veins and intrahepatic collateral veins in 88 groups. Among these, 41 (46.6%) had deep venous collateral channels, 24 (27.3%) had medium venous collateral channels, 9 (10.2%) had superficial venous collateral channels, 5 (5.7%) had portal vein collateral channels, and 9 (10.2%) had intrahepatic venous collateral channels. 3D CE-MRA is important in the clinical diagnosis and treatment planning of BCS and displays hepatic veins, the inferior vena cava system, and collateral vessels.