MXenes have attracted increasing attention due to their unique advantages, excellent electronic conductivity, tunable layer structure, and controllable interfacial chemistry. However, the practical applications of MXenes in energy storage devices are severely limited by the issues of torpid reaction kinetics, limited active sites, and poor material utilization efficiency. Herein, the most-up-to date advances in the rational microstructure design to enhance electrochemical reaction kinetics and energy storage performance of MXene-based materials are comprehensively summarized. This review begins with the preparation and properties of MXenes, classified into fluorine-containing acid etching and fluoride-free etching approaches. Afterwards, the interlayer structure design and interfacial functionalization of MXenes with respect to interlayer spacing and porous structure, terminal groups, and surface defects are summarized. Then the focus turns to the construction of advanced MXene-based heterojunctions based on in situ derivation and surface self-assembly. Based on these microstructure modulating strategies, the state-of-the-art progress of MXene-based applications with respect to supercapacitors, alkali metal-ion batteries, metal-sulfur batteries, and photo/electrocatalysis are highlighted. Finally, the critical challenges and perspectives for the future research of 2D MXene-based nanostructures are highlighted, aiming to present a comprehensive reference for the design of MXene-based electrodes for electrochemical energy storage.