1. A time lapse observation method matching the image capturing area with an image capturing target area on a sample set in advance, capturing an image of the image capturing target area at certain time intervals, to obtain a time lapse image, comprising: before a process to obtain the time lapse image for a first time, capturing an image of a reference area on the sample being a partial area of the image capturing target area or an area in a vicinity of the image capturing target area being a smaller area than the image capturing target area to obtain a reference image; storing a position and a size of the image capturing area in capturing the reference image as a reference position, reference size respectively; and before a process to obtain the time lapse image performed at certain time intervals, setting a position of the image capturing area sequentially at a plurality of different positions in the optical axis direction of an objective including the reference position and capturing an image at each of the plurality of positions to obtain a plurality of comparison target images; and matching the image capturing area in obtaining the time lapse image with the image capturing target area, based on a comparison result of the reference image and the plurality of comparison target images.