Disclosed are a treatment apparatus for denaturing tissue using RF energy having multiple frequencies, a control method thereof, and a treatment method using the same, in which skin treatment is performed using the RF energy with multiple-frequencies different in depth of delivering the RF energy into the tissue. The frequencies of the RF energy may be modulated by the RF modulator. Additionally, the operation of one of several RF generators, which can generate RF energy at the frequency of the RF energy, is determined by the selection of one among multiple RF generators.