MicroRNAs (miRNAs) are closely bound up with the occurrence and deterioration of some cancers, and their early diagnoses have aroused great interest. However, stable and ultra-sensitive real-time detection remains challenge. In this work, we report a strategy for real-time ultrasensitive detection of miRNA-21 by capacitor/enzymatic biofuel cell based self-powered biosensor (EBFC-SPB) with hybridization chain reaction (HCR) for signal amplification. The nitrogen doped dodecahedral hollow carbon (N-DHC) is used for high load, exonuclease III (EXO III)-aided target cells for accurate recognition, and HCR for signal amplification. In addition, the detected signals are further enhanced by a good match with the commercial capacitor, and the real-time portable detection of tumor markers can be achieved by directly reading the data with an Android smartphone. The detection limit of the method is 0.04 fM (S/N = 3) in the linear range of 0.01–5.0 × 103 fM. This method provides reference and theoretical support for the early diagnosis of related tumor markers.