A focus control method able to further correctly control a focal point of an optical system or optical apparatus. A reference system of the system as a whole is set by using a reference pattern for focal point control. A focal point of an optical apparatus for inspecting a sample or measuring a physical quantity of the sample and the focal point of an auto-focus mechanism are matched with the reference system. Then, a displaced object of the auto-focus mechanism is set on a sample surface, a displacement amount of the sample surface from a reference point is measured, and the focal point of an object lens of the optical apparatus is controlled by using the displaced point as an operation point of the control of the auto-focus mechanism. When setting the reference system, the focus is judged by utilizing the Becke effect for the reference pattern.