A high-energy self-powered sensing platform for the ultrasensitive detection of proteins is developed based on enzymatic biofuel cells (EBFCs) by using DNA bioconjugate assisted signal amplification. A nitrogen doped ultra-thin carbon shell/gold nanoparticle (N-UHCS/AuNPs) composite was prepared and applied as an electrode supporting substrate to improve the enzyme load. The biocathode of the self-powered sensor is constructed through the step-by-step modification of N-UHCS/AuNPs and bilirubin oxidase (BOD) on carbon paper (CP). To fabricate the bioanode, SiO2 nanospheres@AuNPs-aptamer (SiO2@AuNPs-ssDNA) bioconjugates were prepared and modified on CP. When there is a target protein, the aptamer recognizes it and causes the SiO2@AuNPs-ssDNA bioconjugate to fall off the bioanode, resulting in a significant increase in the open circuit voltage (EOCV) of the sensing device. Under optimal conditions, the developed biosensor shows a wide linear range of 0.1-2000 ng mL-1 with a low detection limit of 21.5 pg mL-1 (S/N = 3). This work shows an effective assay for the sensitive detection of biomolecules by coupling EBFCs, DNA bioconjugates and the biosensing characteristics of smart nanostructures.