Metabolomics is a new platform based on the comprehensive analysis of low molecular weight metabolites and provides a powerful approach to discover biomarkers in biological systems. Modified Sinisan (MSNS), a traditional Chinese medicine formula, displayed bright prospects in the prevention and therapy of liver injury. However, its molecular mechanism of hepatoprotective effects remains unclear. This paper was designed to explore the effects and potential mechanisms of MSNS against dimethylnitrosamine-induced liver injury. Global metabolic profiling was performed by ultra-performance liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-Q-TOF-MS) in conjunction with multivariate data analysis and pathway analysis. Eleven serum biomarkers were identified and pathway analysis results showed that phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, tryptophan metabolism, retinol metabolism, tyrosine metabolism were perturbed by liver injury. More importantly, MSNS has showed satisfactory pharmacological effect on liver injury through partially regulating the perturbed pathways, correlates well to the biochemical and histopathological detection results. The present study proved that the robust metabolomics approach is promising for unraveling hepatoprotective effects of MSNS and these findings provide new insights into mechanisms of the liver injury, and its pathophysiologic processes.