Herein, polyaniline (PANI) and reduced graphene oxide (rGO) as nanoprobes couple with graphitic carbon nitride to form rGO@g-C3N4-PANI nanocomposite, which exhibits good synergetic enhancement impact on the ECL signal of g-C3N4. Moreover, ZnNiO2 nanoflowers (ZnNiO2 NFs) are firstly used as co-reaction accelerators to remarkably enhance the ECL emission of rGO@g-C3N4-PANI in this work. In the presence of ZnNiO2 NFs, a significant ECL signal enhancement of 15780 a.u. is observed, which is 4 times stronger than that of the rGO@g-C3N4-PANI. Owing to the excellent electronic conductivity and the ability to avoid the deposition of positively charged reduction products, the ZnNiO2 NFs can effectively prevent electrode passivation, thus the rGO@g-C3N4-PANI/ZnNiO2 system emits stable and strong ECL signal. A sensitive ECL sensor has been constructed for the quantitative detection of methotrexate (MTX) of the real blood sample by quenching the ECL signal. Under the optimal conditions, the sensor exhibits a superior linear range from 1 pM to 10 μM and a low detection limit of 0.24 pM (S/N = 3). The proposed ECL signal amplification strategy can be an effective analytical tool for trace detection of targets in biological systems.