Abstract: This study aimed to establish an analytical method capable of simultaneously quantifying the prototype components of Si-Ni-San and screening their metabolites to elucidate its tissue distribution and metabolic characteristics in an ulcerative colitis (UC) mouse model. To this end, an integrated analysis strategy based on UPLC-QqQ-MS was developed and validated, combining the targeted quantification of 12 prototype components with a pseudo-targeted metabolite screening technique based on ion pair list-triggered data-dependent acquisition. Samples were extracted with 80% methanol (100 mg/mL) and processed with internal standards. Separation was achieved on a Waters Acquity UPLC HSS PFP column using a gradient elution with a mobile phase consisting of acetonitrile and 5 mmol/L ammonium acetate containing 0.1% formic acid. Analysis was performed using an electrospray ionization (ESI) source in multiple reaction monitoring mode. Methodological validation confirmed that all parameters met the requirements for bio-sample analysis. Application of this method revealed that the content of Si-Ni-San prototype components in the colon, liver, and kidneys of UC mice was significantly higher than that in healthy mice. Furthermore, the number of phase II metabolites was markedly greater than that of phase I metabolites in all tested samples. The results demonstrate the reliability of the established method and preliminarily reveal the tissue distribution characteristics of Si-Ni-San under UC conditions and its metabolism pattern dominated by phase II conjugation, which provides a methodological basis and experimental data for further in-depth research into its effective target tissues and pharmacodynamic material basis.