Ferroelectric nanocapacitors have attracted intensive research interest due to their novel functionalities and potential application in nanodevices. However, due to the lack of knowledge of domain evolution in isolated nanocapacitors, precise manipulation of topological domain switching in the nanocapacitor is still a challenge. Here, we report unique bubble and cylindrical domains in the well-ordered BiFeO₃ nanocapacitor array. The transformation of bubble, cylindrical and mono domains in isolated ferroelectric nanocapacitor has been demonstrated via scanning probe microscopy (SPM). The bubble domain can be erased to mono domain or written to cylindrical domain and mono domain by positive and negative voltage, respectively. Additionally, the domain evolution rules, which are mainly affected by the depolarization field, have been observed in the nanocapacitors with different domain structures. This work will be helpful in understanding the domain evolution in ferroelectric nanocapacitors and providing guidance on the manipulation of nanoscale topological domains.