Achieving self-assembling structures that exhibit emergent properties and functionalities is one of the holy grails in nanotechnology and holds great promise for a wide range of potential applications. Herein, a self-assembled LuFeO 3 -(1/3)LuFe 2 O 4 -LuFeO 3 heterostructure that consists of two model multiferroics, i.e., hexagonal LuFeO 3 and rhombohedral LuFe 2 O 4 , is reported in single-layer epitaxial LuFeO 3 thin films. Atomic-scale electron microscopy investigations reveal the spontaneous organization of ferroelectric polarization in each building block, which forms a series of polar configurations. Specifically, the charge and lattice of neighboring LuFeO 3 and LuFe 2 O 4 blocks are closely coupled with competing degrees of freedom. A combination of the quantitative analysis of atomically resolved images and spectroscopy with theoretical calculations determines how charge-ordering-induced polarization accommodates charge naturality across the interfaces to reduce the system energy and unravels the formation mechanism of this heterostructure. The results point to the possibilities of generation and control of multiferroic self-assembled systems, which may provide a basis for engineering novel materials with emergent properties.