<p>Tunable light–matter interactions are exhibited by organic low-dimensional crystals, making these crystals a promising platform for organic photonics. However, the precise synthesis of organic low-dimensional crystals remains challenging due to the stochastic nature of molecular nucleation processes. Herein, the directed nucleation process is driven by the introduction of metastable seed-crystals as the trunk, which ultimately leads to branched-array organic heterostructures. The successful formation of organic heterostructures with high-density branched arrays is attributed to the highest attachment energy (<i>E</i>_att(023) = −104.25 kcal mol⁻¹) of the exposed (023) crystal plane during the seed-crystal growth route. Significantly, these as-prepared heterostructures inherently have an ultralow lattice mismatch ratio <i>η</i> of 0.7% between trunk and branch, which contributes to the multi-channel photon transportation. Therefore, this work provides valuable insights into a versatile synthetic strategy for accessing low-dimensional heterostructures for integrated optoelectronics.</p>