The physiological mechanism underlying primary insomnia (PI) is poorly understood. Resting-state functional magnetic resonance imaging (fMRI) has emerged as a powerful tool to explore PI. However, previous studies ignore the dynamics of the brain activity. In the current study, we aimed to explore altered dynamic intrinsic brain activity in PI. Fifty-nine patients with PI and 47 matched healthy controls (HCs) were recruited and underwent resting-state fMRI. The variance of dynamic amplitude of low frequency fluctuation (dALFF) maps across time was calculated to measure the temporal variability of intrinsic brain activity and then compared between patients with PI and HCs. As a result, patients with PI presented increased variance of dALFF in the bilateral hippocampus extending to the parahippocampus, the right putamen and the right anterior insula cortex. In addition, the variance of dALFF in the right putamen was positively correlated with Self-rating Anxiety Scale (SAS) score in PI. Our results revealed increased instability of intrinsic activity in PI.