Giant polyoxomolybdates are a special class of polyoxometalate clusters which can bridge the gap between small molecule clusters and large polymeric entities. Besides, giant polyoxomolybdates also show interesting applications in catalysis, biochemistry, photovoltaic and electronic devices, and other fields. Revealing the evolution route of the reducing species into the final cluster structure and also their further hierarchical self-assembly behaviour is undoubtedly fascinating, aiming to guide the design and synthesis. Herein, we reviewed the self-assembly mechanism study of giant polyoxomolybdate clusters, and the exploration of a new structure and new synthesis methodology is also summarized. Finally, we emphasize the importance of in-operando characterization in revealing the self-assembly mechanism of giant polyoxomolybdates, and especially for the further reconstruction of intermediates into the designable synthesis of new structures.