We report here a new electrochemiluminescence (ECL) approach for detection of single nucleotide polymorphisms (SNPs) based on isothermal cycle-assisted triple-stem probe labeled with Au nanoparticles (NPs) and CdTe NPs. The system is composed of a CdS nanocrystals (NCs) film on glassy carbon electrode (GCE) as ECL emitter attached a double-stem DNA probe labeled with Au NPs. Then, the third stem labeled with CdTe NPs hybridizes with the double-stem DNA to form a triple-stem probe with the two labels near the CdS NCs film. A dual-quenched ECL of CdS NCs film is achieved due to energy transfer (ET) from CdS NCs to Au NPs and CdTe NPs, which makes the sensor exhibit relatively low background. Once the one base mutant DNA (mDNA) sequence as target of SNPs analysis displaces the third stem and hybridizes with the double-stem probe, forcing Au NPs away from the CdS NCs film, an ECL enhancement by the ECL-induced surface plasmon resonance of Au NPs is observed. Furthermore, after an isothermal cycle induced by primer, polymerase, and nicking endonuclease (NEase), a further enhancement of ECL is obtained. Taking advantages of the isothermal circular amplification system and the triple-stem probe architecture which enables turning its high selectivity toward specific target sequences, the reported biosensor shows excellent discrimination capabilities of SNPs with high selectivity and low detection limit (35 aM).