The paper concentrates on the issue of coordination and combined optimization of supply chains. All the member has its own interests, so there are conflicts between members motive and overall system objective. In the paper CAS theory is used as standard paradigm and complexity of the supply chain is analyzed. Case study includes some extreme situations of the supply chain in different levels, namely optimization and coordination problem within operation layer, business layer and enterprise layer. From the study, some rules are summarized to study the problem.