Currently, research mainly focuses on the effects of happy music on the subjective assessment of cognitive reappraisal, but relevant results of the neural mechanism are lacking. By analysing the functional connectivity of microstates based on electroencephalography (EEG), we investigated the effect of cognitive reappraisal combined with happy music on emotional regulation and the dynamic characteristics of brain functional activities. A total of 52 healthy college students were divided into music group and control group. EEG data and behavioural scores were collected during an experiment of cognitive reappraisal combined with happy music. The dynamic time window of the brain functional network was determined by microstate analysis, and the metrics of functional connectivity, clustering coefficient (Cp) and characteristic path length (Lp), were calculated based on the phase-locked value. The arousal of cognitive reappraisal significantly increased (p = 0.005) in music group, but the valence did not change significantly. This suggested that happy music did not affect emotional regulation from the behavioural perspective. Four microstate global templates (A-D) were determined. With happy music, the duration (p = 0.043) and Lp (p = 0.033) of microstate B increased significantly, indicating that the transfection efficiency of the brain network decreased, reflecting a negative effect on cognitive reappraisal. The duration (p = 0.017) of microstate D decreased and of Cp (p < 0.001) increased significantly, indicating that the local information-processing ability of the brain network increased. We conclude that happy music can change the characteristics of brain functional networks and have a positive effect on cognitive reappraisal in specific period. The research provides a certain electrophysiological basis for applying happy music to cognitive reappraisal.