Abstract Saikosaponins (SSs, including SSA, SSB, SSC, and SSD), the major bioactive compounds in the traditional medicine Radix Bupleuri, are emerging agents exhibiting anti-tumor efficacy in several cancers. However, the respective anti-tumor efficacy of these agents and mechanisms in cancers remains unclear. Here, we reported that SSD, among SSs, possessed a significant anti-tumor role across different cancer types in vivo and in vitro by downregulating alternative splicing factors and rewiring oncogenic alternative splicing events. Mechanistically, SSD directly targets PIM1 and blocks the interaction between PIM1 and Myc, and decreases PIM1-mediated Myc phosphorylation at serine 62 and Myc protein stability, resulting in global restraining of Myc-governed alternative splicing factors transcription and inducing oncogenic alternative splicing rewiring. Transcript-specific ablation of SSD-regulated alternative spliced products with CIRSPR-Cas13 or targeting PIM1/Myc with specific small inhibitors significantly desensitizes cancer cells and patient-derived organoids (PDOs) to SSD treatments. These studies demonstrated the potent anti-tumor efficacy of SSD and exposed a PIM1/Myc axis by which SSD modulates the expression of an oncogenic alternative splicing regulatory network that mediates SSD’s anti-tumor role in cancers. Subject terms: Drug development, Cancer Introduction Radix Bupleuri (Chaihu) has been a widely used traditional medicine in Asian countries such as China, Japan, and Korea for over two thousand years for its properties, including anti-inflammation, antitumor, antifebrile, antibacterial, antiviral, and neuroprotective effects [[44]1]. Phytochemical studies have demonstrated that Saikosaponins, especially SSA, SSB2, SSC, and SSD, are the main bioactive compounds [[45]2, [46]3], highlighting their critical roles in Radix Bupleuri in clinical settings. Many studies have reported that Saikosaponins possess potent pharmacological effects such as sedation, antipyretic, antiviral, anti-inflammation, and antitumor properties, consistent with the clinical benefits of Radix Bupleuri [[47]4, [48]5]. Saikosaponins in Radix Bupleuri are complex compounds composed of triterpene aglycone and a carbohydrate part containing 1–13 monosaccharides [[49]6]. Accumulating studies have reported the anti-tumor efficacy of the main Saikosaponins in Radix Bupleuri [[50]7–[51]9], while the individual anti-tumor effects and direct targets remain unclear. Additionally, the different structural characteristics of various Saikosaponins may result in distinct pharmacological activities. Currently, no studies have been reported comparing the differences in anti-tumor effects and cancer type-specific preferences of different Saikosaponins.