Two-dimensional MXenes are promising for various energy-related applications such as energy storage devices and electrocatalysis of water-splitting. MXenes prepared from hydrofluoric (HF) acid etching have been widely reported. Nonetheless, the acute toxicity of HF acid impedes the large-scale fabrication of MXenes and their wide utilization in energy-related applications. It is thus greatly encouraging to explore a more innocuous protocol for MXenes synthesis. Thereby, a universal strategy based on thermal-assisted electrochemical etching route is developed to synthesize MXenes (e.g., Ti2CTx, Cr2CTx, and V2CTx). Furthermore, the cobalt ion doped MXenes show an exceptionally enhanced capability of hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) activity, demonstrating their multifunctionalities, which is comparable to the commercialized catalysts. Moreover, we successfully exploited our MXenes as cathodes for the novel aqueous rechargeable battery, with proficient retention and excellent electrical output performance. This work paves a nontoxic and HF-free route to prepare various MXenes and demonstrates practical applications of the materials.