A thin layer etching apparatus includes an etchant supply unit configured to supply an etchant onto a substrate to etch a thin layer formed on the substrate, a temperature measuring unit configured to measure a temperature of the substrate while an etching process is performed by the etchant, a laser irradiating unit configured to irradiate a first laser beam on a first portion including a central portion of the substrate and to irradiate a second laser beam in a ring shape on a second portion surrounding the first portion so that the temperature of the substrate is maintained at a predetermined temperature during the etching process, and a process control unit configured to control power of the first and second laser beams based on the temperature of the substrate measured by the temperature measuring unit to reduce a temperature difference between the first and second portions of the substrate.