An apparatus and a method for surface treatment of substrates whereby the quality of substrates can be maintained by preventing excessive plasma treatment of substrates. In carrying out the plasma treatment on a surface of the substrate in a reaction chamber, there are provided an emission spectroscopic analysis device or a mass analyzer, and a controller, so that the energy of ions in plasma is controlled to decrease when, e.g., bromine included in the substrate is detected, and the surface treatment to the substrate is controlled to stop when the removal of impurities of the substrate is detected to end. The bromine once separated from the substrate is prevented from adhering again to the substrate and corroding the substrate. Moreover, ions are prevented from being excessively irradiated to the substrate when the removal of impurities ends, thereby reducing damage to the substrate.