Major depressive disorder (MDD) is a prevalent brain disorder affecting more than 2% of the world's population. Due to the lack of well-specific biomarkers, it is difficult to distinguish MDD from other diseases with similar clinical symptoms (such as Alzheimer's disease and cerebral thrombosis). In this work, we provided a strategy to address this issue by constructing a combinatorial biomarker of serum glial fibrillary acidic protein (GFAP) and neurofilament light chain (NFL). To achieve the convenient and sensitive detection of two proteins, we developed an electrochemical immunosandwich sensor using two metal-ion-doped carbon dots (Pb-CDs and Cu-CDs) as probes for signal output. Each probe contains approximately 300 Pb2+ or 200 Cu2+, providing excellent signal amplification. This method achieved detection limits of 0.3 pg mL-1 for GFAP and 0.2 pg mL-1 for NFL, lower than most of the reported detection limits. Analysis of real serum samples showed that the concentration ratio of GFAP to NFL, which is associated with the relative degree of brain inflammation and neurodegeneration, is suitable for not only distinguishing MDD from healthy individuals but also specifically distinguishing MDD from Alzheimer's disease and cerebral thrombosis. The good specificity gives the combinatorial GFAP/NFL biomarker broad application prospects in the screening, diagnosis, and treatment of MDD.