Objectives: This study aims to evaluate the microstructural changes of basal ganglia in neonatal bilirubin encephalopathy (NBE) with two inversion-contrast magnetization-prepared rapid gradient echo (MP2RAGE) sequence. Methods: 22 patients with NBE and 21 healthy, age-matched control neonates were included in this study. Conventional MRI, DWI, and MP2RAGE sequence were performed for all patients and controls. T1 relaxation time of bilateral globus pallidus (GP) and putamen were measured on the T1 mapping images. Results: The 3D T1-weighted high-resolution MP2RAGE contrast image clearly displayed the structure of basal ganglia. Relative hyper-intensity signals were found in bilateral GP on the T1-weighted images in all patients and in 16 (16/21) control neonates. The T1 relaxation time in GP and putamen decreased in the NBE group compared with that in the control group, but the difference was not statistically significant (P > 0.05). The T1-relaxation time ratio of GP and putamen in NBE were shorter than in control neonates (t = 2.38, P < 0.05). The T1 relaxation time ratio of GP and putamen was significantly correlated with the peak level of total serum bilirubin in the NBE group (r = −0.571). Conclusions: The microstructure of basal ganglia changes in NBE. The T1 relaxation time ratio of GP and putamen is associated with serum bilirubin level. The quantitative T1 relaxation time maps obtained with MP2RAGE could be a promising parameter for diagnosis of NBE. Keywords: Neonatal bilirubin encephalopathy, MP2RAGE, T1 relaxation time, Basal ganglia