The present study identified chemical constituents of Honghua Xiaoyao Tablet (HXT) and explored its biological connotation and characteristics on the premenstrual syndrome (PMS) treatment from the "disease-syndrome-symptom" association network. UHPLC-Q Exactive Orbitrap HRMS technology was applied to analyze the chemical constituents in HXT. According to the composition principles, the compatible herbs of HXT were divided into the Shugan Jieyu group, Huoxue Tiaojing group and Yiqi Jianpi group. The candidate targets of the corresponding prescriptions of HXT efficacy groups were collected from the Pharmmapper database and Integrative Pharmacology-based Research Platform of Traditional Chinese Medicine (TCMIP) v2.0. The gene set related to the clinical symptoms included in Traditional Chinese and Western Medicine diagnosis and treatment standards were obtained from SoFDA, GeneCards, DisGeNET, MalaCards and literature published. The "HXT candidate targets-PMS (liver depression, Qi stagnation, and blood stasis syndrome) genes" network was constructed based on the gene interaction information, and further, the core network targets were screened out by topological characteristics of calculating network, and the functional exploration was carried out based on Kyoto Encyclopedia of Genes and Genomes (KEGG) for exploring the therapeutic advantages in PMS treatment of HXT efficacy groups, which were further verified experimentally in vitro. A total of 109 components from HXT were identified, including 20 components from Shugan Jieyu group enriched in the neurological system, estrogen regulation, and "immune-inflammation" related pathways, 77 components from Huoxue Tiaojing group enriched in the blood-circulation system, "immune-inflammation" and estrogen regulation related pathways and 30 components from Yiqi Jianpi group regulating immune inflammation, digestive system, and hormone levels. The biochemical indicator detection demonstrated that both the levels of 5-HT and DA in the hypothalamus tissues and the levels of E₂, NO, VEGF and RLN in the uterine tissues of PMS model rats were lower than those in controls, which the levels of OT, PROG, IL-6, IL-1β and TNF-α in the uterine tissues were increased in PMS group, which were all reversed by the administration of HXT, indicating that this prescription may regulate the synthesis and secretion of estrogen, intervene in neurotransmitter synthesis and signal transduction, reverse the imbalance of "immune-inflammation", and regulate digestive system function through various biological pathways, exerting the liver-smoothing, Qi-regulating, blood-activating and spleen-tonifying comprehensive effects, leading to alleviating the "neuroendocrine-endocrine-immune" system and blood-circulation disorders. The relevant results may provide a reference for clarifying the advantages and efficacy of HXT in treating PMS with liver stagnation, Qi stagnation, and blood stasis syndrome, and exploring its therapeutic advantages. The animal experiment of this study was approved by the Ethics Committee of the Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences (approval number: 2023B248).