In the paper we present a description of complex systems in terms of self-organization processes of prime integer relations. A prime integer relation is an indivisible element made up of integers as the basic constituents following a single organizing principle. The prime integer relations control correlation structures of complex systems and may describe complex systems in a strong scale covariant form. It is possible to geometrize the prime integer relations as two-dimensional patterns and isomorphically express the self-organization processes through transformations of the geometric patterns. As a result, prime integer relations can be measured by corresponding geometric patterns specifying the dynamics of complex systems. Determined by arithmetic only, the self-organization processes of prime integer relations can describe complex systems by information not requiring further explanations. This gives the possibility to develop an irreducible theory of complex systems.