A substrate inspection method includes: generating an electron beam and irradiating the electron beam as a primary electron beam to a substrate as a specimen; inducing at least any of a secondary electron, a reflected electron and a backscattering electron which are emitted from the substrate receiving the primary electron beam, and magnifying and projecting the induced electron as a secondary electron beam so as to form an image of the secondary electron beam; a trajectory of the primary electron beam and a trajectory of the secondary electron beam having an overlapping space and space charge effect of the secondary electron beam occurring in the overlapping space, detecting the image of the secondary electron beam to output a signal representing a state of the substrate; and suppressing aberration caused by the space charge effect in the overlapping space.