Cd-based semiconductor quantum dots (QDs) with size-tunable luminescence and high quantum yield have become the most promising electrochemiluminescence (ECL) emitters. However, their unavoidable biotoxicity limited their applications in bioassays. Here, the nontoxic and economical MoS2 QDs prepared by chemical exfoliation from the bulk MoS2 were first investigated as new ECL emitters, and then the possible luminescence mechanism of MoS2 QDs was studied using ECL-potential curves and differential pulse voltammetry (DPV) methods in detail. With MoS2 QDs as the ECL emitters and triethylamine (TEA) as the efficient coreactant, a practical and label-free aptasensor for lipopolysaccharide (LPS) detection was constructed based on aptamer recognition-driven target-cycling synchronized rolling circle amplification. Comparing to conventional stepwise reactions, this target-cycling synchronized rolling circle amplification achieved more efficient signal amplification and simpler operation. The developed assay for LPS detection demonstrated a wide linear range of 0.1 fg/mL to 50 ng/mL with limit of detection down to 0.07 fg/mL. It is worth mentioning that MoS2 QDs with stable ECL emission exhibited a great application potential in ECL bioanalysis and imaging as a new type of excellent emitter candidates.