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In this article, we investigate the storage enhancement mechanism of stacked multilayer nanocrystallite silicon (nc-Si) structures in a master-equation-based equivalent circuit model. As a theoretical extension from our previous experimental works, we reveal the detail injection sequence of electrons into the multilayer nc-Si structure via a direct tunneling process, and how the retention property is enhanced by the stacked structures. Seeking a further improvement in the multilayer nc-Si-based nonvolatile memory structure, we compare two major approaches for that purpose, i.e. (1) by further increasing the number of stacked layers or (2) by adopting an asymmetric double-layer structure. It is shown that the latter is more promising for achieving better nonvolatile storage property and shows a more effective threshold shifting, while retaining the virtues of direct tunneling process like fast write/erase and low operation voltage. We suggest that these results provide important guides for practical design of memory devices based on multilayer nc-Si floating gate structures.