Related are a method and system for embedding information into encoding information. The method comprises the steps of first embedding the information into an embeddable image or a virtual image using a frequency domain embedding method, and then overlaying the embeddable image or the virtual image into a printed file in need of a variable code or a fixed code using a spatial domain processing method. In this way, the information not perceived by human eyes may be embedded into the encoding information using frequency domain and spatial domain transformation, the counterfeiting difficulty is extremely large, the cost is high, and the anti-counterfeiting purpose is achieved; and furthermore, the printing cost is not increased, thereby being beneficial to wide promotion and application.