In the clinical diagnosis of tumors, a single-marker immunoassay may lead to false results. Thus there is a need for an effective and valid method for the simultaneous measurement of multiple tumor markers. In this work, an efficient fluorescence immunosensor for the simultaneous measurement of CA125 and CA15–3 tumor markers was fabricated by utilizing the high selectivity of magnetic molecularly imprinted polymers (MMIPs) and the high sensitivity of a fluorescence (FL) method. Ni nanoclusters (Ni NCs) and noble Cd nanoclusters (Cd NCs) were introduced as efficient and economic emitters, and magnetic graphene oxide (GO–Fe3O4) was applied as a support material for surface molecularly imprinted polymers. Under the most favorable experimental conditions, the fluorescence intensity of the Cd NCs and Ni NCs gradually increased with increasing concentration of CA125 and CA15–3 antigens at a range of 0.0005–40 U mL−1 , respectively, with a limit of detection (LOD) of 50 μU mL−1 . The developed method had excellent properties including a broad linear range, good reproducibility, and simple operation for the clinical diagnosis of CA 125 and CA 15–3 tumor markers. This molecularly imprinted fluorescence sensor has the potential to be an effective clinical tool for the timely screening of breast cancer in human serum samples and OVCAR-3 and MCF-7 cell lines, and can be applied in clinical diagnostics.