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Engineering of structure and composition is essential but still challenging for electrocatalytic activity modulation. Herein, hybrid nanostructured arrays (HNA) with branched and aligned structures constructed by cobalt selenide (CoSe2) nanotube arrays vertically oriented on carbon cloth with CoNi layered double hydroxide (CoSe2@CoNi LDH HNA) are synthesized by a hydrothermal‐selenization‐hybridization strategy. The branched and hollow structure, as well as the heterointerface between CoSe2 and CoNi LDH guarantee structural stability and sufficient exposure of the surface active sites. More importantly, the strong interaction at the interface can effectively modulate the electronic structure of hybrids through the charge transfer and then improves the reaction kinetics. The resulting branched CoSe2@CoNi LDH HNA as trifunctional catalyst exhibits enhanced electrocatalytic performance toward oxygen evolution/reduction and hydrogen evolution reaction. Consequently, the branched CoSe2@CoNi LDH HNA exhibits low overpotential of 1.58 V at 10 mA cm−2 for water splitting and superior cycling stability (70 h) for rechargeable flexible Zn‐air battery. Theoretical calculations reveal that the construction of heterostructure can effectively lower the reaction barrier as well as improve electrical conductivity, consequently favoring the enhanced electrochemical performance. This work concerning engineering heterostructure and topography‐performance relationship can provide new guidance for the development of multifunctional electrocatalysts. [ABSTRACT FROM AUTHOR]