The precise control of multicomponent complex topological configurations (MCTCs) integrating more than one compound or one crystal-phase with high spatial and angular precision are extremely-challenging due to the anisotropic noncovalent interaction and the undesirable phase separation. Herein, we present a super-stacking self-assembly approach via adjusting the noncovalent interaction strength (| EBghiPE-TCNB (-3.14 kcal mol−1)| > | EBghiPE-TFP (-2.84 kcal mol−1)| > | EBghiPE-OFN (-2.15 kcal mol−1)| > | EBghiPE (-1.33 kcal mol−1)|) for the fine synthesis of molecular heterostructures with various photo-physical properties and low-dimensional morphologies, as well as phase heterostructures with multi-functional optoelectrical characteristics and multi-dimensional morphologies. Notably, the anisotropic noncovalent interaction and the lattice-matching principle facilitate the sequential crystallization and the horizontal/longitudinal growth in the crystal-puzzle process, respectively. This super-stacking self-assembly approach would be easily amenable to precise design and fine synthesis of the desirable organic MCTCs for the integrated optoelectronics.