Transition metal elements (Ni, Cu, Mn, Co and Cr) have been doped into the host structure of molybdenum trioxide via in situ hydrothermal method. The characterizations indicate that Ni and Cu doping has no influence on the structure of the host MoO3 while Co and Cr doping not only cause the crystalline phase transformation but also leads to the morphology change of the doped MoO3. These crystalline and morphology alteration have great impact on the electrochemical performance of the doped samples. The electrochemical tests demonstrate that the specific capacitance and the rate capability are enhanced after Ni, Cu and Mn doping while decline after Co and Cr doping, which may be caused by the structure and morphology change of MoO3 as well as the formation of SEI (solid electrolyte interface) layer after Cr doping. The results manifest that metal ions doping has great impact on the electrochemical property of host materials.