The modularity logistics system is a new concept produced in network era of globalization. The modularity logistics systems have self-organization characteristic. Combining modularity theory with synergetics theory, the association between modularity logistics systems and logistics standardization system was analyzed. And from the self-organization’s point of view, analyzing the internal and external factors of modularity logistics systems, it was identified that the standardization degree and the modularity value of logistics systems are the order parameters among the co-evolutionary of modularity logistics systems. Finally, introducing synergetics to management science, the collaborative management model of modularity logistics systems is put forward based on the public information supporting platform.