Analyzing and detecting endogenous amino acids in blood is of crucial importance for the diagnosis of medical conditions and scientific research. Considering the lack of UV chromophores in most of these analytes and the presence of several interfering substances in plasma, the quantification of quite a few amino acids and related compounds presents certain technical challenges. As a blank plasma matrix lacking these endogenous substances does not exist, the surrogate matrix method is used, as well as isotopic internal standards for calibration, to ensure the accuracy and reliability of the study. Method validation was conducted for 48 target analytes, giving the following results: linearity (R2 at least 0.99), limit of quantification (from 0.65 to 173.44 μM), precision (intra-day and inter-day RSD for LQC ranged from 3.2% to 14.2%, for MQC from 2.0% to 13.6%, and for HQC from 1.6% to 11.3%), accuracy, recovery, and stability of the method (all complied with the guidelines). To further investigate the applicability of this method to large-scale sample analysis, the method was successfully applied to the analysis of amino acids in plasma samples collected from 20 control individuals, demonstrating its wide application scope for clinical diagnosis and metabolic research.