The invention relates to a method for extracting flavonoid and chlorogenic acid from chrysanthemum by ionic liquid aqueous two-phase. The method for extracting the flavonoid and the chlorogenic acid from the chrysanthemum by the ionic liquid aqueous two-phase comprises the following steps that (1) an ionic liquid solution is added to chrysanthemum powder, after the mixture is mixed uniformly, inorganic salt is added to a system, the mixture is fully mixed to form a uniform suspension; (2) the suspension is ultrasonically extracted, and then the mixture is placed silently to form a two-phase system, the upper layer is an ionic liquid phase rich in the flavonoid and the chlorogenic acid, and the lower layer is an aqueous phase with the dissolved inorganic salt, after the liquid separation, an upper layer solution is obtained, that is, a concentrated solution rich in the flavonoid and the chlorogenic acid; and (3) ionic liquid in the concentrated solution rich in the flavonoid and the chlorogenic acid is separated, and extract rich in the flavonoid and the chlorogenic acid is obtained. The method for extracting the flavonoid and the chlorogenic acid from the chrysanthemum by the ionicliquid aqueous two-phase has the characteristics of simple operation, high phase separation speed, high extraction efficiency, low cost and environmental friendliness.