Few studies have focused on the supply chain collaboration under the conditions of intelligent logistics. In this paper, the collaboration architecture of supply chain entities in intelligent logistics is structured to analyze the rules and mechanisms of supply chain entities collaboration, and to provide operation and collaboration standard for supply chain in the future. The architecture includes following sections, which are entities correlation analysis and key criteria choosing, dynamic nonlinear modeling of supply chain system, associated stability analysis with Lyapunov exponent and value simulation. Finally, Markov methods are recommended to study the state transition and feedback mechanism of supply chain system.