In this study, Nitrogen and Sulfur co-doped Graphene Quantum Dots (N, S-GQDs) were synthesized via a pyrolysis approach, utilizing citric acid as the carbon source and L-cysteine as the nitrogen and sulfur sources. These N, S-GQDs were used to develop a novel paper-based electrochemiluminescence (ECL) sensor for the detection of catechol (CC) and tryptophol, two potentially hazardous substances in the environment. Screen printing technology was utilized to construct the ECL sensor on filter paper, incorporating a hydrophobic layer, working and counter electrodes, and a reference electrode. The presence of CC and tryptophol was found to result in a decrease in the ECL intensity of the quantum dots (QDs), this quenching phenomenon is attributed to the oxidation of these substances within the electrochemical system and the subsequent electron transfer from the excited state of the QDs to the oxidation products. The sensor demonstrated a linear detection range for CC and tryptophol from 0.01 to 1000 μM, with detection limits of 0.0082 μM and 0.0066 μM, respectively, and exhibited excellent selectivity, stability, and repeatability. This cost-effective and efficient monitoring technique holds significant promise for environmental and health safety by facilitating the detection of CC and tryptophol, thereby mitigating their potential adverse impacts.