A microscope system and observation control method. An electric zoom consecutively changes a magnification for a sample. A revolver includes a plurality of objective lenses of different magnifications and switches the objective lens placed in an observation optical path to intermittently change the magnification for the sample. A control section calculates a total magnification at which the sample is observed based on a magnification provided by the electric zoom and the magnification of the objective lens currently placed in the observation optical path. The control section operates when the revolver switches the objective lens placed in the observation optical path, to determine a target magnification that is the magnification of the electric zoom required to keep the total magnification obtained after the switching of the objective lens equal to the total magnification obtained before the switching of the objective lens.