Herein, a facile strategy was firstly developed to synthesize ellipsoidal mesoporous silica nanomaterials (MSNs) with well-ordered parallel channels along the short axis. A miniaturized microfluidic device with spiral-shaped channels was then chosen as a straightforward and general platform to produce the corresponding hollow counterparts of MSNs under mild conditions. Such reaction process carried out in a microfluidic system was further demonstrated to be more rapid and efficient than conventional batch method under equivalent experimental conditions. The evolution of hollow structure can be well-tuned by flow rates (i.e., etching time), providing new paradigm for rational design and engineering of anisotropic nanostructures.