Background: Different degrees of T1-weighted (T1W) signal intensities in certain locations on brain magnetic resonance imaging (MRI) are characteristic features of neurological involvement in congenital portosystemic shunt (CPSS). Long-term accumulation of manganese (Mn) as a biomarker can lead to irreversible brain damage. Objectives: The aim of this study was to utilize quantitative brain MRI indicators to characterize brain signal differences in various regions in children with congenital portosystemic shunt. This may contribute to diagnosis, prognosis, and treatment decisions. Patients and Methods: This was a case-control study. Thirty-two patients diagnosed with CPSS based on at least one of the following imaging studies—abdominal ultrasound, Digital Subtraction Angiography (DSA), and Computed Tomography (CT)—and who underwent brain MRI prior to interventional treatment or surgery were included as the Case Group in this study. The age of these patients varied from 22 months to 15 years. Brain MRI of thirty children aged 2 to 15 years, identified without liver or structural diseases, were selected as the Control Group. The brain imaging protocol included an axial spin-echo T1-weighted image (T1WI), an axial T2-weighted image (T2WI), an axial diffusion-weighted imaging (DWI), an axial T2-fluid attenuated inversion recovery (FLAIR) sequence, and a sagittal gradient-echo 3D T1W thin-slice sequence, which can be reconstructed into axial and coronal planes. We utilized quantitative MRI assessment based on the 3D T1-weighted sequence to evaluate intracranial signal differences. The quantitative index was categorized into two types: Globus pallidus-to-frontal subcortical white matter Index (GFI) and anterior pituitary-to-pons Index (API). GFI and API were measured and statistically analyzed on the 3D T1W sequence between the Case Group and the Control Group. GFI of the Case Group was also measured and analyzed between the 3D T1W sequence and the standard T1W sequence. Correlation analysis was applied between the GFI ratios and ammonia levels, as well as between the API ratios and ammonia levels in the Case Group. The duration of the study was more than three months. Results: Significant differences in GFI and API were observed in the Case Group compared with the Control Group (P < 0.01). There was also a statistical difference in GFI between the 3D T1W sequence and the standard T1W sequence (P < 0.01). However, the GFI and API ratios were not correlated with ammonia levels (P > 0.05). The Pearson correlation values were 0.147 and 0.190, respectively. Conclusion: There was a correlation between different brain signals and congenital portosystemic shunt. Quantitative MRI assessment based on the 3D T1-weighted sequence could be used to evaluate these brain signal differences. A longitudinal study with multiple measurements would be beneficial for more accurately assessing such differences, enabling timely interventions, reducing complications, and avoiding lifelong drug therapy.