Ferroelectric topological configurations confined in nanostructures have attracted intensive interest both in fundamental physics and potential applications in non-volatile nanoelectronic devices. However, the preparation approaches such as chemical synthesis and template or electron beam etching inevitably induce damage and contamination; also, these are complicated processes. Herein, by a delicate design of the wetting layer and growth temperature, self-assembled ferroelectric nanoislands were achieved with the BiFeO3/(La,Sr)MnO3/LaAlO3 heterostructure. Based on the thermodynamic analysis, the much lower surface energy (∼0.47 J m-2) of the (La,Sr)MnO3 (∼2-12 nm)/LaAlO3 system than that (∼1.0 J m-2) of BiFeO3 provides the probability for the transformation of layered morphology into nanoislands. From the dynamic perspective, the high growth temperature (∼650-680 °C) helps to step over the energy barrier (∼50 meV per atom) by stimulating the formation of periodically arrayed dislocations at the BiFeO3/(La,Sr)MnO3 interface, which on the one hand releases the epitaxial elastic energy and on the other hand evokes the nucleation of the R-phase nanoisland array. More excitingly, this approach with a wonderful new growth mechanism can also be employed in other ferroelectric model systems such as BaTiO3, which provides a new strategy for the design of novel nanoelectronic devices based on ferroelectric perovskite nanostructures.