A wireless authentication system includes an execution end device and a control end device. When the execution end device and the control end device receive an activation signal, the execution end device generates a time related random code, and transmits the time related random code to the control end device; and the control end device generates a comparison authentication code according to the time related random code, a fixed password and a variable password. When the execution end device determines that the comparison authentication code corresponds to a set of data stored in the execution end device, the execution end device performs a predetermined operation, and the variable password is changed.