Insomnia, affecting the quality of life of millions globally, necessitates urgent and effective treatment strategies. This study conducted a randomized controlled trial to compare traditional and novel treatment methods in a cohort of 60 insomnia patients. Sleep quality and symptoms were assessed using the Pittsburgh Sleep Quality Index (PSQI), Insomnia Severity Index (ISI), and Dysfunctional Beliefs and Attitudes about Sleep Scale (DBAS). Additionally, transcranial Doppler (TCD) technology was employed to measure cerebral hemodynamic parameters. We divided the patients into two groups for insomnia treatment: (1) Control group: oral administration of zopiclone tablets; (2) Treatment group: oral administration of WuMei Decoction. The findings revealed that novel treatment approaches significantly improved sleep quality, disturbances, daytime functionality, and cerebral hemodynamic indicators. Furthermore, identifying 220 potential target genes through systems biology approaches offers new insights into the molecular mechanisms of insomnia and opportunities for drug development.