1. A pattern inspection apparatus comprising: an electron scanning unit configured to scan a surface of a sample with an electron beam and to detect secondary electrons emitted from the surface of the sample; a signal processor configured to create a SEM image of the sample on the basis of a relation between irradiation position with the amount of the secondary electrons; a storage configured to store distortion amount data representing a magnitude of positional displacement in a scanning direction of the electron beam, the positional displacement being caused by distortion of the SEM image; and a controller configured to match design data of the sample with the SEM image by adjusting at least one of the design data and the SEM image on the basis of the distortion amount data, wherein the controller includes: a measurement region setting unit configured to set a measurement region on a pattern of the design data for the sample with reference to the design data; a measurement region adjusting unit configured to adjust positional coordinates of the measurement region on the design data on the basis of the distortion amount data and to place the adjusted measurement region on the SEM image; and a measurement unit configured to measure dimensions of a pattern inside the measurement region on the SEM image.