Hierarchical nanozeolites are highly desired for heavy oil conversion because of their fast mass transfer, good site accessibility, and short diffusion length compared with their conventional counterparts. Here, we provide a facile amino acid-assisted strategy to synthesize hierarchical ZSM-5 (MFI) zeolite nanocrystals by two-step crystallization in a concentrated gel system. Strikingly, each virus-like zeolite nanoparticle with abundant interconnected intracrystalline mesopores is a high-quality single crystal that is defect-free as confirmed by electron diffraction and NMR analysis. By utilizing advanced electron microscopy techniques, we have studied the evolution process of single-crystalline hierarchical ZSM-5 nanocrystals that involves oriented aggregation of protozeolitic nanoparticles formed at low temperature followed by intraparticle ripening at high temperature. The as-prepared hierarchical Ni@ZSM-5 catalysts exhibit superior catalytic performance in hydro-deoxygenation of stearic acid and palm oil.