A single-crystal X-ray structure analysis apparatus capable of surely and easily performing a single-crystal X-ray structure analysis using a crystalline sponge, and an analysis method and a sample holder unit thereof are provided. There are provided a sample holder that holds a sample; a goniometer that rotationally moves, the sample holder 250 being attached to the goniometer; an X-ray irradiation section that irradiates the X-rays from the X-ray source to the sample held by the sample holder 250 attached to the goniometer, wherein the sample holder 250 comprises a porous complex crystal capable of soaking the sample in a plurality of fine pores formed therein, and the applicator comprises a space for soaking the sample in the porous complex crystal of the sample holder 250.