To provide a microscopic imaging apparatus capable of accurately measuring an object to be inspected having drastic variance in luminance, and to provide a biological material observation system with which the microscopic imaging apparatus is used.

The microscopic imaging apparatus is provided with a stage for holding the object to be inspected, an illuminating means for illuminating the object, an imaging means for photographing the image of the object, and a moving means for relatively moving the stage and the imaging means, and the imaging means is provided with an imager capable of imaging by a time-delay integration system, and in the case of imaging (S1 and S3) the object by the imaging means plural times so as to capture a plurality of sheet images, an exposure time for generating the accumulated charge in the imager is varied whenever capturing a different image, and the plurality of sheet images are synthesized (S4) to one sheet image.