Disclosed herein is a method of manufacturing a semiconductor device having a recess channel structure, which prevents misalignment of a source/drain, thereby being capable of achieving an improvement in the drive-ability of a gate and preventing a degradation in characteristics of the semiconductor device due to a hot carrier effect. The method comprises the steps of forming a threshold voltage adjustment ion layer having a predetermined depth in an active region of a silicon substrate, implanting source/drain forming ions into the silicon substrate on the threshold voltage adjustment ion layer formed in the silicon substrate, forming a mask, which defines a recess trench forming region, on the silicon substrate, after completing the implantation of the source/drain forming ions, forming recess trenches by etching the silicon substrate to a predetermined depth using the mask as an etching mask, depositing polysilicon on the silicon substrate to a thickness sufficient to bury the recess trenches, and forming a gate electrode through planarization of the deposited polysilicon.