The molecular fingerprint sensing technology based on metasurface has unique attraction in the biomedical field. However, in the terahertz (THz) band, existing metasurface designs based on multi-pixel or angle multiplexing usually require more analyte amount or possess a narrower tuning bandwidth. Here, we propose a novel single-pixel graphene metasurface. Based on the synchronous voltage tuning, this metasurface enables ultra-wideband ( $$\sim$$ 1.5 THz) fingerprint enhancement sensing of trace analytes, including chiral optical isomers, with a limit of detection (LoD) ≤ 0.64 μg/mm2. The enhancement of the fingerprint signal ( $$\sim$$ 17.4 dB) originates from the electromagnetically induced transparency (EIT) effect excited by the metasurface, and the ideal overlap between the light field constrained by single-layer graphene (SLG) and ultra-thin analyte. Meanwhile, due to the unique nonlinear enhancement mechanism in graphene tuning, the absorption envelope distortion is inevitable. To solve this problem, a universal fingerprint spectrum inversion model is developed for the first time, and the restoration of standard fingerprints reaches Rmax2 ≥ 0.99. In addition, the asynchronous voltage tuning of the metasurface provides an opportunity for realizing the dynamic reconfiguration of EIT resonance and the slow light modulation in the broadband range. This work builds a bridge for ultra-wideband THz fingerprint sensing of trace analytes, and has potential applications in active spatial light modulators, slow light devices and dynamic imaging equipments.