Objective To explore the clinical efficacy of Modified Suanzaoren Decoction for chronic insomnia disorder （CID） patients and the neuroimaging mechanism of resting-state functional magnetic resonance imaging （rs-fMRI）. Methods From October 2020 to January 2022， 39 CID patients with yin-deficiency and fire-hyperactivity were selected from the Clinic of Inner Mongolia Autonomous Region Mental Health Center， Community Clinic and WeChat Official Account as research objects. Patients were given a 4-week treatment with Modified Suanzaoren Decoction. The scores of the Insomnia Severity Index （ISI）， Pittsburgh Sleep Quality Index （PSQI）， Hamilton Anxiety Scale （HAMA）， 24-item Hamilton Depression Scale （HAMD-24）， Repeatable Battery for Assessment of Neuropsychological Status （RBANS）， as well as polysomnography and rs-fMRI were compared before and after treatment in patients. Pearson correlation was used to analyze the correlation between testing time series mean and PSQI， ISI， HAMA， and HAMD-24 reduction rates. Results Twenty-seven patients with CID were finally included and after treatment with Modified Suanzaoren Decoction， the total PSQI score ［（9.85±3.48） vs （12.82±2.92）］， ISI score ［（9.44±5.66） vs （17.30±5.45）］， HAMA score ［（6.67±3.89） vs （11.19±4.71）］， and HAMD-24 score ［（6.70±4.48） vs （11.52±6.44）］ of the patients were all lower than before treatment， and the differences were statistically significant （all P ＜ 0.05）. The total score of RBANS （98.72±9.30） was higher than before treatment （88.92±8.59）， and the difference was statistically significant （P ＜ 0.05）. There was no statistically significant difference in the results of polysomnography after treatment compared to before treatment （P＞ 0.05）. The functional connections of the hippocampus， thalamus， posterior cingulate gyrus， and orbital frontal gyrus changed， and the differences were statistically significant （all P＜0.05）. The decrease in functional connection between the left posterior cingulate gyrus and the left frontal gyrus was positively correlated with the reduction rate of HAMD-24 （r=0.422， P=0.028）， while the decrease in functional connection between the left orbital frontal gyrus and the left anterior cingulate gyrus and the paracingulate gyrus was negatively correlated with the reduction rate of HAMD-24 （r=-0.399， P=0.039）， and the differences were statistically significant. Conclusions After treatment with Modified Suanzaoren Decoction， the insomnia symptoms and emotions of CID patients improve significantly. The mechanism is related to the regulation of abnormal functional activities in areas such as the hippocampus， thalamus， posterior cingulate gyrus， and orbital frontal gyrus.