Tumor targeting delivery system has been suggested as an attractive strategy against tumor progression. And combination chemotherapy is essential and effective in preventing gastric cancer. Hesperitin (HE) has been suggested to exhibit anticancer ability through inducing apoptosis in many tumors without obvious toxicity, and it exerts synergistic anti-cancer ability with other drugs. Clinical application of daunorubicin (DA) in treatment of various cancers has been restricted. Targeted delivery of anti-cancer drugs could reduce their off-target effects and promote their efficacy. In our paper, HE and DA co-loaded methoxy poly (ethylene glycol)-poly(ε-caprolactone) (MPEG-PCL) nanoparticles were prepared through an assembly method. The morphology, particle size (about 38 nm), zeta potential, release profile in vitro, cell proliferation and cytotoxicity effects were investigated. The results suggested that HE and DA could be efficiently loaded into MPEG-PCL nanoparticles synchronously, and in vitro study indicated that they could be released from the nanoparticles in an extended period. in vitro, HE/DA/MPEG-PCL exerted an enhanced cytotoxicity and high apoptosis-inducing activities of gastric cancer cells. Importantly, HE/DA/MPEG-PCL exhibited better cancer targeting and accumulation, enhancing the anti-tumor efficacy with little toxicity. Together, HE/DA/MPEG-PCL promoted the drug target on tumor site with preferable anti-tumor effects, which could be a promising therapeutic strategy against human gastric cancer.