A method of applying virtual makeup adapted for an electronic device having a virtual makeup electronic system is provided. The method of applying virtual makeup includes the steps: receiving a plurality of facial images of different angles of a face to construct a 3D facial model; recording a real-time facial image of the face, and the 3D facial model varies with the face in real time according to the real-time facial image; providing 3D virtual makeup to the 3D facial model; converting the 3D virtual makeup to 2D virtual makeup according to a position and an angle of the real-time facial image; combining the real-time facial image and the 2D virtual makeup to generate an output image; and displaying the output image. A virtual makeup electronic system and an electronic device having a virtual makeup electronic system are further provided.