In this study, we present a simple but effective fluorescent system for highly sensitive and versatile sensing of 2,4,6-trinitrotoluene (TNT) using few layered planar MoS2 quantum dots (QDs) as reporters. Excitation-independent emitting MoS2 QDs were first fabricated by using the proposed ultrasonic-hydrothermal-based top-down method assisted by carbon-free hydroxylamine hydrochloride. The obtained pristine MoS2 QDs were then modified with cysteine for introducing amino groups as TNT binding sites. The as-prepared MoS2 QDs possess a planar structure, which can more adequately interact with flat aromatic TNT molecules due to π-π attraction and decreased steric effects, compared with traditional spherical/quasi-spherical QDs. As a result, they exhibit extremely high sensitivity for TNT sensing (1 nM and 2 ng for solution and substrate assay, respectively). The common ions containing in environmental water samples do not interfere with the sensing. Furthermore, the QDs-decorated test paper shows an instantaneous (within 1 min) response to trace amounts of deposited TNT, and the fluorescence quenching can even be well-visualized by the naked eye. Because of favorable analytical performances, the proposed MoS2 QDs-based TNT sensing system has potential applications in both environmental water monitoring and security screening.