Polygala japonica Houtt. (P. japonica), a member of the Polygala genus in the Polygalaceae family, has been historically utilized in traditional folk medicine as an expectorant, anti-inflammatory, anti-bacterial, and anti-depressant agent. This paper systematically reviews the latest research in botany, traditional uses, phytochemistry, pharmacology, and pharmacokinetics, aiming to provide a scientific foundation for the future development and application of P. japonica and to explore its potential value comprehensively. Approximately 86 compounds have been isolated from P. japonica, with triterpenoid saponins being the most prevalent and bioactive components. Extensive pharmacological activities of P. japonica extracts or compounds have been confirmed in vivo and in vitro, including anti-inflammatory, anti-depressant, neuroprotective, anti-obesity, anti-apoptotic, and skin-protective effects. Additionally, P. japonica has demonstrated significant curative effects and relatively clear pharmacological mechanisms in treating inflammatory and nervous system diseases. Specific components of its primary triterpenoid saponins are rapidly absorbed in the body. This review advocates for deeper scientific research on P. japonica, noting that most current research remains in its early stages and many reported biological activities require further clinical validation. Despite this, the traditional medical use of P. japonica across various cultures attests to its broad application value. Presently, the pharmacological activities of P. japonica extracts and compounds provide a scientific basis for its traditional uses. Future research must ensure the safety and effectiveness of P. japonica through in-depth pharmacokinetic studies, and the establishment of a refined and standardized quality evaluation system is essential for its clinical development and application.