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Music can liberate positive power of pain management in fibromyalgia (FM) patients through multiple neural modulation. However, traditional brain research preferred to investigate the neural characteristics of music-induced analgesia (MIA) based on the seed points of functional activation, which limits the understanding of the connection states of the whole-brain functional synchronization network involved in FM's music listening. The current study aimed to investigate the whole-brain network functional connectivity (FC) differences of resting-state functional magnetic resonance imaging (RS-fMRI) before and after music listening in FM patients using a data-driven analysis approach. Using a publicly available dataset, the RS-fMRI data from 20 FM patients were analyzed. A network-based FC approach was applied to compare intra- and inter-network FC changes across the visual network (VN), somatosensory network (SMN), ventral attention network (VAN), default mode network (DMN), and subcortical network (SC). After music listening, FM patients exhibited significant reduction in evaluation of pain intensity (PI), and also exhibited changed intra-network FC within the VAN and VN; changed inter-network FC between the VAN and DMN, between the VN and SMN or DMN, between the SMN and DMN, and between the VN and SMN or DMN, respectively. What's more, correlations were found between post-pre changes in subjective pain ratings and post-pre changes in network FC. Positive correlations were found between PI's reduction and the increase of inter-network FC between the right fusiform (VN) and left middle insula (SMN), and also found between the reduction of pain unpleasantness (PU) and the increase of inter-network FC between the left middle insula (SMN) and left posterior occipital cortex (DMN). The network FC results here provided new evidence to the inter/intra-networks in VN, SMN, VAN, DMN, and subcortical network, explaining that FM patients may generate cognitive processing from bottom to top and emotion regulation from top to down to realize their MIA.