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Rational design of hollow mesoporous silicas with distinctive morphology has attracted considerable interest for their promising applications of different functions. Herein, we reported hollow mesoporous silica ellipsoids with quasiperiodic cocoon-shape, and fully investigated the evolution of external morphology and interior structure with solution concentrations. However, synthetic theories used so far hardly provide reasonable explanation. Therefore, a morphogenetic mechanism upon interfacial destabilization dynamics is proposed based on the experimental results, in which unstable interfaces of emulsions influenced by harmonic perturbations are employed as secondary templates for the nonequilibrium deposition/diffusion of rod-like micelles, explaining well the controllability of the morphology.