As the highly complex logistics system, container terminal logistics systems play an increasingly important role in modern international logistics, and therefore their scheduling and decision-making process of much significance to the operation and competitiveness of harbors. In this paper, the handling, stacking and transportation in CTLS are regarded as a kind of generalized computing and compared with the working in general computer systems, whereupon the Harvard architecture and AnyLogic agent-based computing paradigm are fused to model the operational processing of CTLS, and the kernel thoughts in computer organization, architecture and operating system are introduced into CTLS to support and evaluate container terminal planning, scheduling and decision-making.