The invention discloses an ultra-pure adaptive nonlinear control system for an internal thermally coupled distillation column. The system comprises a filed intelligent instrument and a DCS system which are directly connected with the internal thermally coupled distillation column, wherein the DCS system comprises a storage device, a control station, and an upper computer; the filed intelligent instrument is connected with the storage device, the control station, and the upper computer; the upper computer comprises an ultra-pure adaptive nonlinear controller which is used for calculating and outputting the control variable value of the internal thermally coupled distillation column; and the ultra-pure adaptive nonlinear controller comprises a component deduction module, a model parameter adaptive correction module, and an adaptive ultra-pure control law solving module. The invention also provides an ultra-pure adaptive nonlinear control method for the internal thermally coupled distillation column. The control system and the control method can well process the strong nonlinear characteristics of the ultra-pure internal thermally coupled distillation column, and have efficient online operating rate and extremely good servo tracking control effect and interference suppression effect.