A molecularly imprinted electrochemiluminescence sensor (MIECLS) is constructed to selectively detect clenbuterol (CLB) based on boron nitride quantum dots@gold nanoflowers/silver nanowires (BNQDs@AuNFs/AgNWs). The abundant amino and hydroxyl groups on the surface of the BNQDs generate an electrostatic self-assembly effect with the multi-tipped spatial structure of AuNFs, constituting a novel nanoscale co-reaction accelerator (NCRA) with high activity and large load capacity. An NCRA embedded in the network structure of the AgNW luminophores significantly promotes the reduction of peroxydisulfate (S2O82−) to sulfate anion radicals (SO4−•) through the catalysis of amino groups and boron radicals (B•) and the electron acceleration of AuNFs while also reducing the reaction distance between SO4−• and AgNWs−•, realizing the multiple synergistic amplification of the electrochemiluminescence (ECL) signal. Imprinted cavities in the molecularly imprinted polymers (MIPs) prepared by electropolymerization can generate a “blocking-effect” by recognizing CLB, realizing ECL signal quenching. Analytical results indicate that the established MIECLS detects CLB in a line concentration range of 0.5–50000 nM and detection limit of 0.00693 nM. The spiked recoveries are 85.90%–97.77%, with the relative standard deviations (RSD) under 5.1%, consistent with those of high-performance liquid chromatography (HPLC). This work demonstrates that an efficient NCRA can significantly enhance the output of the ECL signal in collaboration with the original luminophore, providing a new method to realize the ultra-detection of targeted substances by MIECLS.