The controlled self-assembly of organic heterostructures (OHSs) with precisely defined compositions, architectures, and interfaces, have largely remained a challenge. Herein, we introduce an effective approach to accurately construct three types of axial branching OHSs including unilateral axial OHSs, bilateral single-branching axial OHSs and bilateral multi-branching axial OHSs through modulating hierarchical charge-transfer intermolecular interactions and sequential crystal nucleation rate on account of the two different cocrystals with the low lattice mismatching rate of ~ 2.2%. The present work opens an avenue for rationally designing and finely synthesizing more kinds of OHSs.