Controlled manipulation of photons/electrons at micro/nanoscale holds the key to the development of versatile optoelectronics devices. However, current photonics devices are primarily constructed from simple low‐dimensional structures, which suffer from limited structural design freedom due to the planar processing scheme, impeding further performance improvement and functionality upgrades. Herein, the first 3D hydrogen‐bonded organic framework (HOF) branched homostructure with spatial positioned multi‐input/output optical channels for 3D photon manipulation is reported. The free‐standing 3D HOF branched homostructures are prepared by a steric engineering strategy, which involves a multinucleation‐assisted growth mechanism. The hierarchical Y‐type and X‐type HOF homostructures exhibit asymmetrical photon transport behaviors, showing applications in optical logic gates with single or dual ON/OFF functionality, respectively. Moreover, the 3D HOF branched homostructure with multiple spatially distributed input/output optical channels displays spatial asymmetric photon transport, which functions as spatial photonic signal logics. These results offer a novel strategy for the development of HOF‐based photonic devices with 3D photon manipulation.