Hollow polyhedral cages hold great potential in the application of nanotechnological and biomedical fileds. Understanding the formation mechanism of these self-assembled structures could provide guidance for the rational design of the desired polyhedral cages. Here, by constructing kinetic network models from extensive coarse-grained molecular dynamics simulations, we elucidated the formation mechanism of the dodecahedral cage, which is formed by the self-assembly of patchy particles. We found that the dodecahedral cage is formed through the aggregate size increasing followed by structure rearrangement. Based on this mechanistic understanding, we improved the productivity of the dodecahedral cage through rational design of the patch arrangement of patchy particles, which promotes the structure rearrangement process. Our results demonstrate that it should be a feasible strategy to achieve rational design of desired nanostructures via the kinetic analysis. We anticipate that this methodology could be extended to other self-assembly systems for the fabrication of functional nanomaterials.