PKMYT1 represents a promising therapeutic target for CCNE1-amplified cancers due to its synthetic lethal relationship with CCNE1. By leveraging a structure-based drug design strategy, we successfully developed a series of novel, highly potent and selective PKMYT1 inhibitors. Notably, compound 20 exhibited potent antiproliferative activity in CCNE1-amplified cell lines while showing minimal effects on their wild-type counterparts, along with exceptional selectivity across a broad kinase panel. Moreover, its favorable pharmacokinetic properties contributed to robust antitumor efficacy in an HCC1569 xenograft model. Furthermore, two prodrug derivatives of compound 20 were designed to improve aqueous solubility, achieving dose-proportional systemic exposure in rats during dose-escalation preclinical toxicity studies. Additionally, the combination of prodrug 22 with TrodelvyⓇ, a TROP2 ADC, demonstrated synergistic antitumor activity in triple-negative breast cancer MDA-MB-231 xenograft models.