Functionalized porous carbon materials with hierarchical structure and developed porosity coming from natural and renewable biomass have been attracting tremendous attention recently. In this work, we present a facile and scalable method to synthesize MnO2 loaded carbonaceous aerogel (MnO2@CA) composites via the hydrothermal carbonaceous (HTC) process. We employ two reaction systems of the mixed metal ion precursors to study the optimal selective adsorption and further reaction of MnO2 precursor on CA. Our experimental results show that the system containing KMnO4 and Na2S2O3·5H2O exhibits better electrochemical properties compared with the reaction system of MnSO4·H2O and (NH4)2S2O8. For the former, the obtained MnO2@CA displays the specific capacitance of 123.5 F·g(-1). The enhanced supercapacitance of MnO2@CA nanocomposites could be ascribed to both electrochemical contributions of the loaded MnO2 nanoparticles and the porous structure of three-dimensional carbonaceous aerogels. This study not only indicates that it is vital for the reaction systems to match with porous carbonaceous materials, but also offers a new fabrication strategy to prepare lightweight and high-performance materials that can be used in energy storage devices.