Herein, we are reporting the synthesis of flower - like MoS2, spherical MnO2 and their nanocomposites using versatile hydrothermal approach. The structural and morphological studies of the synthesized samples have been performed using X-ray diffraction (XRD), Transmission electron microscopy (TEM) and Field emission scanning electron microscopy (FESEM). Thermal gravimetric analysis (TGA), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) have also been carried out to evaluate the thermal stability, elemental composition and functional groups present in the samples, respectively. Surface area and pore size distribution are determined by the Brunauer–Emmett–Teller (BET) analysis. The effect of molar ratio of MnO2 and MoS2 on the electrochemical properties of MnO2@MoS2 nanocomposite has been investigated thoroughly using conventional three electrodes set-up in 2 M KOH aqueous electrolyte at room temperature. From the experimental results, the synthesized nanocomposite with 3:1 molar ratio of MnO2 and MoS2 exhibits higher BET specific surface area (~133 m2/g), optimum pore size distribution, specific capacitance of 352 F g−1 at 1 A g−1, ~72% capacity retention and ~88% coulombic efficiency after 2000 successive cycles at 3 A g−1 in 2 M KOH. This sample exhibits smaller relaxation time constant (τₒ = 150 ms) and higher diffusion coefficient (Da = 162.99 × 10−10 cm2 s−1). The detail correlation between electrochemical behavior and structural characterization of as synthesized nanocomposites has been described and discussed in this paper.