As the structural foundation of microtubules, tubulin represents a pivotal molecular target in anticancer drug discovery. The design and evaluation of small-molecule tubulin polymerization inhibitors continues to be a productive strategy for identifying next-generation chemotherapeutic agents. Based on systematic structural analysis of known tubulin inhibitors targeting the colchicine-binding site and available computational tubulin-ligand models, a focused library of 3-aryl-5-(3,4,5-trimethoxyphenyl)-5H-pyrrolo[2,3-b]pyrazine derivatives was rationally designed and synthesized as candidate tubulin polymerization inhibitors. Among these, compound 10u demonstrated the most pronounced antiproliferative activity, with IC50 values spanning 0.085-0.13 μM across three human cancer cell lines (Huh7, HeLa, and A549). Mechanistic studies indicated that 10u potently suppresses tubulin polymerization, dismantles the intracellular microtubule network, arrests the cell cycle at the G2/M phase, and subsequently induces apoptotic cell death. In an orthotopic Huh7 mouse model, 10u significantly inhibited tumor growth without eliciting observable systemic toxicity. Collectively, these results highlight 10u as a promising tubulin polymerization inhibitor with potent dual-phase anticancer activity, supporting its further development as a potential therapeutic agent.