The present invention relates to a substrate inspection apparatus for inspecting a pattern formed on a substrate by irradiating a charged particle beam onto the substrate. The substrate inspection apparatus comprises: an electron beam apparatus including a charged particle beam source for emitting a charged particle beam, a primary optical system for irradiating the charged particle beam onto the substrate, a secondary optical system into which a secondary charged particle beam is introduced, the secondary charged particle beam being emitted from the substrate by an irradiation of the charged particle beam, a detection system for detecting the secondary charged particle beam introduced into said secondary optical system and outputting as an electric signal, and a process control system for processing and evaluating the electric signal; a stage unit for holding the substrate and moving the substrate relatively to said electron beam apparatus; a working chamber capable of shielding at least an upper region of the stage unit form outside to control under desired atmosphere; and a substrate load-unload mechanism for transferring the substrate into or out of the stage.