The invention provides a water-cooled motor controller for a high power density electric vehicle. In the controller, an opening is formed at the bottom of one side of a shell, and a water cooling radiator is arranged at the opening; a power module, a direct current bus support capacitor, a pre-electrified resistor, a main relay and a current sensor are arranged in the shell respectively; the power module is arranged on the upper surface of the water cooling radiator; the direct current bus support capacitor, the pre-electrified resistor, the main relay and the current sensor are fixed in the shell respectively through bolts; the power module, the direct current bus support capacitor and the main relay are connected through a conflux busbar to form a high-voltage loop; a power factor correction capacitor is fixed on the conflux busbar; a drive circuit board which is used for a power module is arranged above the power module; a separator and a control circuit board are arranged above the drive circuit board sequentially; and a plurality of power cable connectors used for assembling power cables pass through the lateral wall of the shell. The water-cooled motor controller has the advantages of flexible and convenient operation process, strong radiation capability, high power density, good electromagnetic compatibility and safe and reliable use effect.