Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related death, which is demanding powerful diagnosis tools. Although the traditionally used serological biomarker alpha-fetoprotein (AFP) cannot meet the requirement of accurate diagnosis, its isoform alpha-fetoprotein L3 (AFP-L3) ratio in total AFP is emerging as a highly specific alternative. The routine electrophoretic blotting methods for analyzing AFP-L3 isoform ratio are reliable but often lack speediness, sensitivity, or accuracy. Herein, an elemental mass spectrometric strategy was established to simultaneously detect total AFP and AFP-L3 for the accurate HCC diagnosis. The metal isotopes inside colloidal gold nanoparticle (AuNP) and colloidal silver nanoparticle (AgNP) reporters were used to sensitively detect total AFP and AFP-L3, respectively. AFP-L3 and total AFP were accurately and simultaneously detected with the limits of detection (LODs) of 0.1 ng mL-1 and 0.2 ng mL-1, respectively. The proposed method was successfully validated in a series of human serum samples. The assay procedure was greatly simplified and less time-consuming for the AFP-L3 isoform ratio evaluation, when compared to clinical routine chromatographic/electrophoretic methods. Thanks to the highly multiplex ability of mass spectrometry, the proposed method provides great potential for the analysis of multiple isoforms of various disease biomarkers.