Ferroelectric nanoislands have attracted intensive research interest due to their size effect induced exotic physical properties and potential applications in non-volatile ferroelectric memories. However, the self-assembly growth of highly ordered ferroelectric nanoisland arrays is still a challenge. Here, by patterning a LaAlO3 substrate with etched nanocavities to provide preferential nucleation sites, highly ordered self-assembled BiFeO3 nanoisland arrays with robust ferroelectric topological quad-domain configurations were achieved. From the thermodynamic and kinetic perspectives, three factors are critical for achieving highly ordered self-assembled nanoisland arrays, that is, preferential nucleation sites, an appropriate relationship between the surface energy and the interface energy, and the growth rate difference of films. This approach can also be employed for the self-assembly growth of nanoisland arrays in other ferroelectric materials, which facilitates the design of ferroelectric nanostructure-based nanodevices.