Rational exploration of efficient, inexpensive, and robust electrocatalysts is critical for the efficient water splitting. Conjugated conductive metal–organic frameworks (cMOFs) with multicomponent layered double hydroxides (LDHs) to construct bifunctional heterostructure catalysts are considered as an efficient but complicated strategy. Here, the fabrication of a cMOF/LDH hetero‐nanotree array catalyst (CoNiRu‐NT) coupled with monodispersed ruthenium (Ru) sites via a controllable grafted‐growth strategy is reported. Rich‐amino hexaiminotriphenylene linkers coordinate with the LDH nanotrunk to form cMOF nanobranches, providing numerous anchoring sites to precisely confine and stabilize RuN4 sites. Moreover, monodispersed and reduced Ru moieties facilitate H2O adsorption and dissociation, and the heterointerface between the cMOF and the LDH further modifies the chemical and electronic structures. Optimized CoNiRu‐NT displays a significant increase in electrochemical water‐splitting properties in alkaline media, affording low overpotentials of 22 mV at 10 mA cm−2 and 255 mV at 20 mA cm−2 for the hydrogen evolution reaction and oxygen evolution reaction, respectively. In an actual electrochemical system, CoNiRu‐NT drives an overall water splitting at a low cell voltage of 1.47 V to reach 10 mA cm−2. This performance is comparable to that of pure noble‐metal‐based materials and superior to most reported MOF‐based catalysts. A conductive metal–organic framework (cMOF)/layered double hydroxide (LDH) hetero‐nanotree structure coupled with monodisperse Ru sites is constructed via a controllable grafted‐growth strategy. Based on a competitive coordination process, RuN sites are precisely anchored by rich‐amino organic linkers. The chemical and electronic structure of the hetero‐nanotree catalysts are well modified and lead to a superior overall water‐splitting performance in alkaline media.