Natural cytotoxic peptides (NCPs) are emerging sources of novel anticancer chemotherapeutics. Especially, Melittin, which is the major component of bee venom and the first-in-class NCP, has been considered as a promising anticancer scaffold. Nevertheless, as a classical linear, cationic, amphipathic, and membrane-lytic peptide, Melittin may be easily degraded by proteases, suffering from poor stability, moderate anticancer durability, and severe hemolysis. In this study, applying the terminal modification and hybridization strategies, ten Melittin-based derivatives were designed, synthesized, and investigated for their anticancer potential. The robust and economic synthetic method, in vitro anticancer efficiency, time-kill kinetics, serum stability, anti-migration activity, hemolysis effects, and anticancer mechanism were explored. As expected, the Melittin-based derivatives exhibited highly potent cytotoxicity against all six tested cancer cell lines. In particular, compared with natural Melittin, the derived peptides LJ-5 containing both N-terminal acetylation and C-terminal hydrazidation, and LJ-6, the methotrexate MTX-GFLG-Melittin conjugate exhibited significantly improved proteolytic stability, more durable anticancer efficiency, higher anti-migration activity, as well as reduced hemolysis effects. Besides, it was further verified that LJ-5 and LJ-6 could efficiently disrupt the integrity of cancer cell membrane, localize to the mitochondria and rapidly reduce the mitochondrial membrane potential of cancer cells. Collectively, the economic synthetic method and stability-guided optimization were conducted on Melittin, affording hydrolysis-resistant LJ-5 and LJ-6 that may serve as anticancer candidates and useful references for further optimizations of cytotoxic peptides.