Lily-Ziziphi Spinosae Semen decoction (LZ) is known for its blood nourishing, mind calming, body sedation, and sleep promoting effects in traditional Chinese medicine. However, its material basis and underlying mechanisms have not yet been clearly defined. This study applies liquid chromatography-mass spectrometry, network pharmacology, and animal studies to reveal the material basis and sleep-improving mechanisms of LZ. The mixed decoction (LZ-ME) and single decoction (LZ-SE) were prepared to study their chemical components. Network pharmacology was used to predict the sleep-improving targets and signaling pathways of LZ. ICR mice were intragastrically administered saline (NC), melatonin (positive control group, 0.50 mg/kg), low (12.90 g/kg), medium (25.70 g/kg), and high (38.60 g/kg) dose of LZ-ME and LZ-SH for 30 days. The results showed that LZ-ME could prolong the sleep duration and shorten the sleep latency in sodium barbiturate induced mice model. The results of chemical composition showed that total polysaccharides, total flavonoids, total saponins, and total alkaloids in LZ-ME were significantly higher than those in LZ-SE (177.20%, 82.34%, 30.58%, and 11.66%, respectively). A total of 58 chemical components were identified by ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS), and 8 representative difference components of LZ-ME and LZ-SE were found. LZ-ME significantly increased tumor necrosis factor-α (TNF-α) in mice serum and neurotransmitter γ-aminobutyric acid (GABA) levels in mice hippocampus, decreased dopamine (DA) and glutamate (Glu) levels in mice hippocampus (P < 0.05). Furthermore, LZ-ME up-regulated the abundance of the beneficial bacteria Lactobacillus and Eubacterium_R, down-regulated the abundance of the harmful bacteria Lachnospiraceae etc. The polysaccharides, flavonoids (spinosin and 6‴-feruloylspinosin) and saponins (jujuboside A and jujuboside B) were the main material bases for the sleep-promoting effects of LZ. These compounds may directly enhance levels of the GABA, reduced levels of Glu and DA and improve TNF-α levels. And they also may indirectly regulate GABA levels by influencing the relative abundance of Lactobacillus and Eubacterium.