Time lapse observation method includes: before a process to obtain a first time lapse image, capturing an image of a reference area on a sample being a partial area of a target area or an area in a vicinity of the target area being a smaller area than the target area to obtain a reference image; storing a position of a capturing area in capturing the reference image as a reference position; before a process to obtain the time lapse image performed, setting a position of the capturing area sequentially at different positions in the optical axis direction of an objective including the reference position and capturing an image at each of the positions to obtain comparison target images; and matching the capturing area with the target area, based on a comparison result of the reference image and the comparison target images.