An amphiphilic small molecular drug self-delivery system was designed by linking a hydrophilic topoisomerase I inhibitor irinotecan (Ir) with a lipophilic cytotoxic enediyne (EDY) antibiotic through an ester bond. The maleimide-based EDY with a pendant carboxyl group was synthesized in four steps from commercially available reagents. The EDY compound possesses the ability to generate radical intermediates at physiological temperature as demonstrated by electron spin resonance analysis and further causes DNA-cleavage and tumor cell suppression. The self-delivery system prepared by the combination of two anticancer drugs, EDY and Ir, formed nanoparticles' self-assembly with a size of around 60 nm in aqueous solution, enabling the drugs to accumulate in tumor tissues through the enhanced permeability and retention effect. With high drug loading capacity (100%), the Ir-EDY nanoparticles entered tumor cells through endocytosis and possessed strong synergistic effects, inducing tumor cell death through the cell apoptosis pathway efficiently.