High sensitivity, good signal repeatability, and facile fabrication of flexible surface enhanced Raman scattering (SERS) substrates are common pursuits of researchers for the detection of probe molecules in a complex environment. However, fragile adhesion between the noble-metal nanoparticles and substrate material, low selectivity, and complex fabrication process on a large scale limit SERS technology for wide-ranging applications. Herein, we propose a scalable and cost-effective strategy to a fabricate sensitive and mechanically stable flexible Ti3C2Tx MXene@graphene oxide/Au nanoclusters (MG/AuNCs) fiber SERS substrate from wet spinning and subsequent in situ reduction processes. The use of MG fiber provides good flexibility (114 MPa) and charge transfer enhancement (chemical mechanism, CM) for a SERS sensor and allows further in situ growth of AuNCs on its surface to build highly sensitive hot spots (electromagnetic mechanism, EM), promoting the durability and SERS performance of the substrate in complex environments. Therefore, the formed flexible MG/AuNCs-1 fiber exhibits a low detection limit of 1 × 10-11 M with a 2.01 × 109 enhancement factor (EFexp), signal repeatability (RSD = 9.80%), and time retention (remains 75% after 90 days of storage) for R6G molecules. Furthermore, the l-cysteine-modified MG/AuNCs-1 fiber realized the trace and selective detection of trinitrotoluene (TNT) molecules (0.1 μM) via Meisenheimer complex formation, even by sampling the TNT molecules at a fingerprint or sample bag. These findings fill the gap in the large-scale fabrication of high-performance 2D materials/precious-metal particle composite SERS substrates, with the expectation of pushing flexible SERS sensors toward wider applications.