In resistance welding of thermoplastic composites, a stainless-steel (SS) heating element (HE) is usually applied with current to provide heat to melt the thermoplastic polymer and remains at the joint. In this study, electrospinning technique was proposed to produce nanofiber films on the SS HE to achieve the hole pre-filling in the mesh and to provide a resin-rich zone in the bondline to enhance resin impregnation and void reduction, which improved the mechanical interlocking of the joints. The lap shear strength (LSS) of welded joints with nanofiber films was increased by 2.3 times to 36.98 MPa in comparison to the film-free joints and the indefinite fatigue life of the joint was reported at 20% of the static LSS. Taguchi method and Analysis of Variance approach were used to investigate the influence of the process parameters on the LSS. A comparative analysis of the welding curves, defects distributions, and fractographic evolutions was carried out for welded joints with and without the nanofiber films. With nanofiber films, the main failure modes of the joints changed from HE debonding to interlayer debonding.