Background: The underlying neurological mechanism of acupuncture treatment in migraine without aura (MwoA) remains unclear. Therefore, we explored the dynamic alterations of intrinsic brain activity and effective connectivity in patients with MwoA after acupuncture treatment.Methods:The fMRI scans were separately obtained at baseline, after the first and after the 12th acupuncture sessions in 40 patients with MwoA. The acupuncture treatments were finished within 6 weeks as twice a week. 36 matched healthy controls (HCs) were recruited and performed once fMRI scan. The dynamic amplitude of low-frequency fluctuation (dALFF) and dynamic granger causality analysis(GCA) were used to analyze the difference of different time points in patients with MwoA. The correlation analyses were performed in dALFF variability, dynamic effective connectivity (DEC) variability with clinical variables in patients with MwoA.Results:Compared with HCs, Patients with MwoA at baseline showed decreased dALFF variability in regions within rostral ventromedial medulla (RVM), the superior lobe of left cerebellum (Cerebelum_Crus1_L), the right inferior frontal gyrus, triangular part (IFGtriang.R), the right median cingulate and paracingulate gyri (DCG.R), the right precuneus (PCUN.R), and the left inferior parietal, supramarginal and angular gyri (IPL.L), increased dALFF variability only in the left inferior occipital gyrus (IOG.L). After acupuncture treatment, the decreased dALFF variability of the RVM, Cerebelum_Crus1_L , and PCUN.R progressively recovered, the RVM revealed gradually increased DEC variability to the right middle frontal gyrus (MFG.R), the left insula (INS.L), the right precentral gyrus (PreCG.R), and the right supramarginal gyrus (SMG.R). And enhanced DEC variability from the right fusiform gyrus (FFG.R) to RVM. Furthermore, the increased DEC variability were found from Cerebelum_Crus1_L to the left middle occipital gyrus (MOG.L) and the left precentral gyrus (PreCG.L), from PCUN.R to the right thalamus (THA.R). These dALFF variabilities were significantly positive correlated with frequency of migraine attack and negative correlated with disease duration at baseline, dynamic GCA coefficients were significantly positive correlated with Migraine-Specific Quality of Life Questionnaire (MSQ) score, negative correlated with frequency of migraine attack and visual analog scale (VAS) score postacupuncture treatment.Conclusions: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.Trial registration: ChiCTR, ChiCTR1900023105. Registered 11 May 2019, http://www.chictr.org.cn/showproj.aspx?proj=36959.