We explored the dynamic alterations of intrinsic brain activity and effective connectivity after acupuncture treatment to investigate the underlying neurological mechanism of acupuncture treatment in patients with migraine without aura (MwoA). The fMRI scans were separately obtained at baseline, after the first and after the 12th acupuncture sessions in 40 patients with MwoA. Compared with HCs, patients with MwoA showed mostly decreased dynamic amplitude of low-frequency fluctuation (dALFF) variability in regions with differences. After acupuncture treatment, the decreased dALFF variability of the rostral ventromedial medulla (RVM), the superior lobe of left cerebellum (Cerebelum_Crus1_L), and the right precuneus (PCUN.R) progressively recovered. The RVM revealed gradually increased dynamic effective connectivity (DEC) variability outflow to the right middle frontal gyrus, the left insula, the right precentral gyrus, and the right supramarginal gyrus, and enhanced DEC variability from the right fusiform gyrus inflow to RVM. Furthermore, the increased DEC variability were found from Cerebelum_Crus1_L outflow to the left middle occipital gyrus and the left precentral gyrus, from PCUN.R outflow to the right thalamus. These dALFF variabilities were positive correlated with frequency of migraine attack and negative correlated with disease duration, dynamic GCA coefficients were positive correlated with Migraine-Specific Quality of Life Questionnaire score, negative correlated with frequency of migraine attack and visual analog scale score postacupuncture treatment. Our results provide insight into dynamic alterations from the perspective of dynamic local brain activity and effective connectivity for the understanding mechanisms of cumulative therapeutic effect of acupuncture in patients with MwoA.