Polyamine conjugated flavonoid with a naphthalene moiety (ZYY14) displayed excellent therapeutic activity against hepatocellular carcinoma. In this study, three different series of novel flavonoid-polyamine conjugates were designed and screened against tumor cell lines. The structure-activity relationship study demonstrated the importance of the naphthalene moiety (as the B-ring), the basic side chains in the A-ring, and the methoxy group linked to the C-ring. The optimized compound 9b displayed better antitumor potency in vitro and in vivo than the lead compound ZYY14. Fluorescent assays revealed that 9b could enter cancer cells via polyamine transporter (PAT) and locate in mitochondria and endoplasmic reticulum. Compound 9b and ZYY14 demonstrated similar apoptotic mechanism in the cytotoxicity studies and stimulated the expression of apoptosis-related proteins, such as p-p38, p-JNK, p53 and Bax. In addition, 9b can initiate autophagy which inhibited the occurrence of apoptosis. Thus, 9b can be used as a valuable lead for the future development of antitumor agents.