Insomnia, a sleep-disordered disease, is characterized by difficulty in falling asleep, decrease of sleep quality and sleep time, decline of memory and attention. Ziziphi Spinosae Semen (ZSS) is one of the important “medicine-food” herbs for insomnia and anxiety. In this research, the sedative and hypnotic effects of ZSS extract (ZSSE) was evaluated by animal experiment, and the potential active components and related mechanism were further analyzed by using metabonomics and network pharmacology techniques. The results showed that ZSSE could cooperate with the subthreshold dose of barbital sodium in the hypnotic effect of mice, and the high-dose group (1 g/kg) significantly prolonged the sleep time of mice induced by barbital sodium (P < 0.01). A total of 200 compounds were obtained from ZSSE by liquid chromatography-mass spectrometry (LC-MS/MS), including triterpenoids, flavonoids, alkaloids, organic acids, fatty acyls, and among them 113 active components were screened. Network pharmacological analysis indicated that kaempferol, boldine, apigenin and ursolic acid may be the potential active ingredients of ZSSE in the treatment of insomnia. Protein-protein interaction (PPI) networks analysis showed that AKT serine/threonine kinase 1 (AKT1), catalase (CAT), prostaglandin-endoperoxide synthase 2 (PTGS2) and heme oxygenase 1 (HMOX1) were the main key targets. Gene Ontology (GO) enrichment analysis showed that these targets were mainly involved in steroid metabolic process, hormone level regulation and metabolism, synaptic membrane, neuronal cell body, heme binding, postsynaptic neurotransmitter receptor activity and neurotransmitter receptor activity. The enrichment analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway showed that the sedative and hypnotic effects of ZSSE might be closely related to signaling pathways such as steroid hormone biosynthesis, neuroactive ligand-receptor interaction, HIF-1 signaling pathway, calcium signaling pathway, dopaminergic synapse, cAMP signaling pathway and cholinergic synapse. This study revealed the potential active components and mechanism of ZSSE in the treatment of insomnia, and provided a theoretical basis for the development and utilization of ZSS.