Recently, neuroinflammation was proposed as an important role in fibromyalgia. However, the correlation between neuroinflammation and functional connection in fibromyalgia patients remained unclear. Fibromyalgia patients and healthy control participants were recruited to investigate the mechanism of fibromyalgia. Independent component analysis, diffusion kurtosis MRI and cortical thickness estimation were applied in this study. The finding implied that neuroinflammation and structural change of brain were associated with the abnormal functional connection in fibromyalgia.