An image pickup system includes: a light source portion configured to emit first illumination light with a first wavelength band and second illumination light with a second wavelength band on a short-wavelength side of the first wavelength band； an image pickup portion configured to perform image pickup of return light from an object； an image generating portion configured to generate a first image corresponding to return light of the first illumination light and a second image corresponding to return light of the second illumination light, each of which corresponds to one field, and sequentially output the first image and the second image； a synchronization processing portion configured to accumulate the images corresponding to a plurality of fields and simultaneously output the accumulated images corresponding to the plurality of fields, selectively assigning the images to first to third channels of a display apparatus； and a control portion configured to perform control for setting image assignment to and image update frequency for the first to third channels based on one or more evaluation values acquired from the images generated by the image generating portion.
