An electric motor control system and a method of digitally controlling rotation speed of an electric motor are disclosed. The method includes the following steps: a user's demand for the rotation speed of the electric motor is received through a graphical user interface, a preset rotation speed table is automatically calculated, pulse width modulation signals are generated according to the presetrotation speed meter so as to control electric motor operation, actual rotation speed of the electric motor during operation is read when the pulse width modulation signals are at a plurality of different duty ratios, and the preset rotation speed table includes preset rotational speed corresponding to the pulse width modulation signals at a plurality of fixed duty ratios. The motor control systemand the method of digitally controlling rotation speed of the electric motor disclosed in the invention can be used for flexibly setting the rotation speed of the electric motor according to the user's demand, and therefore design and debugging costs and cycles can be reduced.