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The novel strain-driven morphotropic phase boundary (MPB) in highly strained BiFeO3thin films is characterized by well-ordered mixed phase nanodomains (MPNs). Through scanning probe microscopy and synchrotron X-ray diffraction, eight structural variants of the MPNs are identified. Detailed polarization configurations within the MPNs are resolved using angular-dependent piezoelectric force microscopy. Guided by the obtained results, deterministic manipulation of the MPNs has been demonstrated by controlling the motion of the local probe. These findings are important for an in-depth understanding of the ultrahigh electromechanical response arising from phase transformation between competing phases, enabling future explorations on the electronic structure, magnetoelectricity, and other functionalities in this new MPB system.