Electrochemiluminescence (ECL) detection has attracted increasing attention as a promising analytical approach. A considerable number of studies showed that ECL intensity can be definitely improved by resonance energy transfer (RET), while the RET efficiency is strongly dependent on the distance between exited donors and acceptors. Herein we disclose for the first time a highly enhanced RET strategy to promote the energy transfer efficiency by coencapsulating the donor (Ru­(bpy)32+)/acceptor (CdTe quantum dots, CdTe QDs) pairs into a silica nanosphere. Plenty of Ru­(bpy)32+ and CdTe QDs closely packed inside a single nanosphere greatly shortens the electron-transfer path and increases the RET probability, therefore significantly enhancing the luminous efficiency. Further combining with molecularly imprinting technique, we develop a novel ECL sensor for ultrasensitive and highly selective detection of target molecules. Proof of concept experiments showed that extremely low detection limits of subfg/mL (S/N = 3) with broad linear ranges (fg/mL to ng/mL) could be obtained for detection of two kinds of mycotoxins (α-ergocryptine and ochratoxin A) that are recognized as potential health hazards at very low concentrations. This strategy combining enhanced RET system and molecularly imprinting technique, represents a versatile ECL platform toward low-cost, rapid, ultrasensitive, and highly selective detection of target molecules in diverse applications.