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The electrochemiluminescence (ECL) aptasensor was prepared for the detection of Mucin 1 based on its specific recognition by aptamer immobilized on multi‐functionalized graphene oxide nanocomposite, which was prepared with N‐(4‐aminobutyl)‐N‐ethylisoluminol (ABEI) and aptamer chemically bound to the surface of magnetic GO (nanoFe3O4@GO). ABEI and aptamer acted as the electrochemiluminophore and the capture device for Mucin 1 respectively. NanoFe3O4@GO brought multi‐functionalized graphene oxide nanocomposite attracted on the surface of magnetic glass carbon electrode through magnetism, enabled all the ABEI immobilized electrochemically active due to its good conductivity and thus then facilitated the sensitive detection of Mucin 1. In addition, the ECL aptasensor can be prepared through a one‐step process. Under optimal conditions, the ECL intensity of the aptasensor decreased proportionally to the logarithmic concentrations of Mucin 1 in the range of 0.005–1000 ng mL−1. This aptasensor displays good specificity, stability, reproducibility and application. This method has a large potential because such a multi‐functionalized graphene oxide nanocomposite also may be applied to other ECL‐based aptasensors.