To provide an aligning method of a charged particle beam exposure apparatus in which error can be suppressed in an alignment, and to provide a charged particle beam aligner.

The aligning method of the exposure apparatus comprises a stage 120 moving while mounting a sensitive substrate 100, a stage position measuring instrument 160, an optical system 110 with a lens and a deflector for irradiating the sensitive substrate selectively with a charged particle beam, and a means 140 for detecting an alignment mark put on the sensitive substrate. The alignment mark is detected while predicting the stage position at an arbitrary time after receiving information from the stage position measuring instrument, and the sensitive substrate is aligned using a predicted value of the stage position just at the detection timing of the alignment mark.