A microscope apparatus (1A) includes a biological sample table (11) that supports the biological sample (B), an objective lens (12) disposed to face the biological sample table (11), a laser light source (13) that outputs light with which the biological sample (B) is irradiated via the objective lens (12), a shape measurement unit (20) that acquires a surface shape of the biological sample (B), a control unit (40) that generates aberration correction hologram data for correcting an aberration caused by the surface shape of the biological sample (B) on the basis of information acquired in the shape measurement unit (20), a first spatial light modulator (33) to which a hologram based on the aberration correction hologram data is presented and that modulates the light output from the laser light source (31), and a photodetector (37) that detects an intensity of light to be detected (L2) generated in the biological sample (B). Thus, a microscope apparatus and an image acquisition method capable of suppressing a decrease in condensing intensity of irradiation light inside a biological sample and spreading of a condensing shape are realized.