Development of selective, ultra-sensitive, rapid and facile methods for the detection of chemical residues of toxic pesticides and hazardous chemicals are quite important in food safety, environmental monitoring and safeguarding public health. Herein, we presented a fluorescent turn-on aptasensor based on sulphur-doped graphene quantum dot (S-GQD) utilizing specific recognition and binding property of aptamer for the ultra-sensitive and selective detection of omethoate (OM) which is a systemic organophosphorus pesticide. The detection method is based on tuning aggregation-disaggregation mechanism of S-GQD by way of conformational alteration of the recognition probe. Fluorescence ‘turn-on’ process includes aggregation-induced quenching of S-GQD with aptamer via S-GQD-aptamer complex formation and its subsequent fluorescence recovery with the addition of OM by structural switching of S-GQD-aptamer complex to aptamer-omethoate complex. The reported ‘switch-on’ aptasensor has exhibited a low limit of detection of 0.001 ppm with high selectivity for OM over other pesticides.