The invention discloses an electron beam current energy density distribution measurement system and method. The electron beam current energy density distribution measurement system comprises an electron beam generating, deflecting and focusing device, an electron beam energy density measurement device, a controller and a data processing device; the electron beam generating, deflecting and focusingdevice is used for controlling generation, focusing and deflection of an electron beam; the electron beam energy density measurement device is used for measuring the intensity of an electron beam current leaking from a top right-angle gap of the electron beam energy density measurement device, and recording a deflection signal of the electron beam; the controller is used for controlling the electron beam generating, deflecting and focusing device to generating, focusing and deflecting the electron beam, and meanwhile controlling the electron beam energy density measurement device to collect an electron beam intensity signal and record the deflection signal of the electron beam; and the data processing device is used for constructing the electron beam intensity signal into a two-dimensional data matrix according to the deflection signal of the electron beam, and calculating electron beam energy density distribution by adopting a second-order differential method. The system simplifies processing of a measuring device, and irregular electron beam current energy density distribution can also be accurately measured without presuming circumference symmetry of the electron beam energy density.