Precise synthesis of high‐quality, sophisticated heterostructures by ordered assembly of small nanomaterials is a key step to gain advanced materials that have elaborate functionalities, collective properties, and enhanced stabilities for mitigating the energy and environment crisis. Intricating in the structure, size, and shape of nanomaterials, ordered assembly of isotropic or anisotropic nanoscale building blocks to create specified heterostructures remains challenging, owing to the extraordinary challenges in design of lattice topology of distinct nanounits and in control of their crystallization, growth, and assembly mechanism/kinetics. Herein, the emerging methodologies to prepare a diversity of ordered heterostructures with strengthened particle–particle interaction are examined and synergistic properties are enhanced. It is aimed to unlock the principles to regulate the geometrical and electronic properties of these intriguing kinds of heterostructures for respective sustainable energy and environmental applications. Current challenges and opportunities in customization of ordered heterostructure at the nanoscale and atomic level are also discussed.