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Background Evidence suggests that transcranial direct current stimulation (tDCS) combined with repetitive transcranial magnetic stimulation (rTMS) is more effective than either modality alone. However, the underlying neural mechanisms remain unclear.Objective To explore the effects of combined tDCS-rTMS on cortical functional networks and neural regulation processes in chronic insomnia.Methods In this randomised, double-blind, sham-controlled trial, 111 adults with chronic insomnia were allocated to real tDCS+real rTMS or sham tDCS+real rTMS. Participants received 20 weekday sessions over 4 weeks. Of these, 106 completed treatment and 103 provided functional near-infrared spectroscopy (fNIRS) data meeting predefined quality criteria. fNIRS measured oxygenated haemoglobin (Oxy-Hb) responses in prefrontal and temporal regions during a verbal fluency task (VFT) before and after treatment. The primary outcome was haemodynamic activation; secondary outcomes were functional connectivity and sleep quality.Findings Sleep quality improved in both groups, with significantly greater reduction in Pittsburgh Sleep Quality Index (PSQI) scores in the real tDCS+real rTMS group (p<0.05). No between-group differences were observed in VFT performance. However, the combined stimulation group showed significantly increased Oxy-Hb responses across multiple fronto-temporal channels, particularly in bilateral temporal regions, and greater enhancement in mean functional connectivity (p<0.05). Both interventions were well tolerated, with no serious adverse events.Conclusions This study provides neuroimaging evidence that combined tDCS and rTMS may improve chronic insomnia by enhancing activation of fronto-temporal cortices and strengthening inter-regional functional connectivity. These findings offer objective support for the clinical efficacy of the combined stimulation protocol, link neurophysiological changes to treatment optimisation and suggest potential advantages of this approach for neuromodulation-based therapeutic strategies.Clinical implications These findings suggest that tDCS combined with rTMS may represent a feasible and well tolerated non-pharmacological strategy for chronic insomnia, with potential advantages over rTMS alone at both clinical and neurophysiological levels.Trial registration number This study was registered as a clinical trial with the China Clinical Trial Registration Centre (ChiCTR2100052681).