MoS2 and ZnS quantum dots (QDs) were synthesized and applied as labels in magnetic immunoassays for the determination of myeloperoxidase (MPO) and osteopontin (OPN) via single-particle mode inductively coupled plasma mass spectrometry (ICP-MS). Primary MPO antibodies and primary OPN antibodies were captured by amino-modified magnetic nanoparticles, and the target biomarkers (MPO and OPN) were extracted and then specifically labeled with MoS2 QD-secondary MPO antibody and ZnS QD-secondary OPN antibody conjugates, respectively. MoS2 and ZnS QDs were employed as determination signal probes for ICP-MS measurements. Under the optimized conditions, the limits of detection obtained by magnetic immunoassay for MoS2 and ZnS QD-labeled MPO and OPN were 0.004 and 0.005 ng mL-1, respectively. The linear ranges for MPO and OPN were 0.01–50 and 0.02–50 ng mL-1, respectively. From six replicates, the relative standard deviations of MPO and OPN were found to be 3.5% and 3.2%, respectively. The proposed strategy was applied to determine the MPO and OPN levels in real human serum samples.