Resistance welding technology is an effective solution for connecting thermoplastic composites. However, limited research on non-uniform distribution of interfacial temperature and complex evolution mechanism of phase-change molding hinders its application. This reliance on traditional experimental and trial-and-error methods severely impedes its development. Therefore, this study employed a novel cross-scale numerical simulation method, being applied for the first time in the field of resistance welding for elucidating the underlying mechanism of joint formation through multi-component phase transformation. The constructed model accurately represented the transient heat transfer of a realistic wire mesh structure in three dimensions, while incorporating complex gradient effects arising from both spatial and temporal variations in heating element temperature due to air interference. Further, melting, flow, and consolidation behavior of the resin matrix in resistance welding of carbon fiber/polyetheretherketone (CF/PEEK) thermoplastic composite was investigated herein at a mesoscopic scale. To accomplish this objective, a three-phase flow spatial forming and evolution model for resistance welding was developed at the mesoscopic scale by integrating principles from fluid dynamics. Interestingly, introduction of an air phase reinstated the spatial voids formation and flow in resistance welding, providing robust evidence for the initiation mechanism of internal defects. Moreover, this study revealed variations in the melting mode of PEEK resin across different regions within the weld and highlighted distinct distributions of voids resulting from uneven heat transfer. The interfacial phenomenon and flow diffusion mechanism between components in resistance welding tests were further verified and discussed through analyzing scanning electron microscopy and energy dispersive spectroscopy results. Temporal and spatial correlation in void distribution within the welding zone was observed, which was found to be consistent with simulation results. Specifically, with the progress of the welding process, air near the wire mesh gradually dispersed into the laminate, with significantly more voids at weld seam edges than in central regions. This research methodology based on stepwise scale reduction offers a promising avenue for investigating resistance welding and other connection forming applications, in particular, within the context of engineering underlying logical behavior.