Three-dimensional self-supported cathode nanoarchitectures are the key to develop high-performance thin film lithium-ion microbatteries and flexible lithium-ion batteries. In this work, we have developed a facile “hydrothermal lithiation” strategy to prepare vertically aligned porous LiMn2O4 nanowall arrays, comprising highly crystallized spinel nanoparticles, on various conductive substrates without high temperature treatment. The “hydrothermal lithiation” can effectively convert Mn3O4 spinel nanowall arrays into LiMn2O4 spinel nanowall arrays without severe morphology change. The binder-free three-dimensional porous LiMn2O4 nanowall arrays exhibit high specific reversible capacity up to 131 mAh g−1 (or 0.29mAh cm−2) as well as outstanding cycling stability and rate capability, making them promising as cathodes for both three-dimensional thin film lithium-ion microbatteries and flexible lithium-ion batteries. A flexible lithium-ion full cell is demonstrated by using LiMn2O4 nanowall arrays on carbon cloth as the cathode and Li4Ti5O12 nanowall arrays on carbon cloth as the anode. The flexible Li4Ti5O12//LiMn2O4 full cell device, employing three-dimensional nanoarchitectures for both cathode and anode, can deliver specific reversible capacities of 124.8 mAh g−1 (based on the weight of cathode material) at 1 C and 92.1mAh g−1 at 20 C with excellent cycle performance. Our work demonstrates the great potential for flexible energy storage technology using low cost fabrication method of nanoarchitectures.