The invention provides an encoding method of invisible image ciphers. The encoding method comprises the following steps that: a system receives a specified picture and an encryption request from a client end, and performs cell processing on the picture, and equally divides cells in an orderly way; CMYK four-color value calculation is performed on the equally-divided cells, so that a color value database of different numerical values can be formed; the cells are repeatedly extracted according to rules so as to be subjected to paired color value difference comparison, and comparison results are assigned with 1 or 0 based on preset rules, so that a brand new set of source value database with an internal logic basis can be formed; and information to be encrypted is stored in the source value database in a grouped manner. With the encoding method adopted, invisible code information of codes is invisible. The information of a traditional two-dimensional code is stored through a geometrical feature, and the geometrical feature is exposed to naked eyes apparently, and as a result, defects of high possibility of being cracked, copied and stolen of the traditional two-dimensional code exist, while, with the encoding method of the invention adopted, the defects can be eliminated. According to the encoding method, the specified information of the client end is adopted as a key to match comparison value parameters, and therefore, various kinds of situations can be provided, and people can be prevented from reversely recognizing and extracting information.