Fibromyalgia (FM), chronic widespread pain, exhibits spontaneous pain without external stimuli and is associated with altered brain activities during resting state. To understand the topological features of brain network in FM, we employed persistent homology which is a multiple scale network modeling framework not requiring thresholding. Spontaneous magnetoencephalography (MEG) activity was recorded in 19 healthy controls (HCs) and 18 FM patients. Barcode, single linkage dendrogram and single linkage matrix were generated based on the proposed modeling framework. In theta band, the slope of decrease in the number of connected components in barcodes showed steeper in HC, suggesting FM patients had decreased global connectivity. FM patients had reduced connectivity within default mode network, between middle/inferior temporal gyrus and visual cortex. The longer pain duration was correlated with reduced connectivity between inferior temporal gyrus and visual cortex. Our findings demonstrated that the aberrant resting state network could be associated with dysfunction of sensory processing in chronic pain. The spontaneous nature of FM pain may accrue to disruption of resting state network.