Herein, we present the development of an ultra-sensitive immobilization-free homogeneous electrochemiluminescence (ECL) biosensor, leveraging the electrostatic repulsion between a negatively charged indium tin oxide (ITO) electrode and DNA and exonuclease I (Exo I)-powered signal amplification, to achieve highly efficient detection of thrombin. Specifically, the aptamer and the complementary DNA engage in the formation of a double-stranded DNA (dsDNA) complex. This negatively charged dsDNA structure subsequently associates with a positively charged ECL indicator, namely ruthenium phenanthroline (Ru(phen)32+), resulting in the generation of the dsDNA-Ru(phen)32+ ECL probe. The negatively charged dsDNA-Ru(phen)32+ experiences electrostatic repulsion from the negatively charged ITO electrode, resulting in a low ECL signal. Nonetheless, upon the addition of thrombin, the aptamer preferentially binds to thrombin, triggering the releases of the embedded Ru(phen)32+ facilitated by Exo I and hence resulting in a robust and enhanced ECL signal. The amplified ECL signal is linearly correlated with the logarithm of thrombin concentration within a detection range spanning from 10 fmol/mL to 50 pmol/mL, with a remarkable detection limit of 3.21 fmol/mL. This strategy eliminates the need for cumbersome labeling steps, avoids the electrode modification process, overcoming the low immobilization efficiency of aptamers and poor signal transduction of indicators labeled at the end of DNA.