Technological improvements in material handling at seaports is a complex, multi-stage process with a large, inhomogeneous structure of input-output parameters, and a possible return to initial calculation stages. Mathematical modeling and numerical experiment, replacing a real experiment, contribute to speed up this process and bring it to a higher quality level. The analysis of the research works reveals a new process approach-based methodology for improving cargo handling technologies in operating port. This approach became a base for the mathematical models construction for the import cargo handling technology at the container terminal under the preferences of the Free Port of Vladivostok. The mathematical models implementation of import container flow control system at sea terminal under the real conditions (the base version) and proposed conditions (with use of warehousezoning logistic technology according to the Pareto principle within the preliminary informing of maritime transport regulatory authorities) is performed on the discrete event simulation platform-MATLAB / Simulink. The universal description of possible import freight routes through the terminal provides low labor intensity of the experiments planning and changing the transport and technological pattern of the analyzed process in a more flexible way. The results of numerical experiments on evaluating the container terminal operation showed a significant advantage of the proposed flowchart of import container cargo handling (reduction of cargo storage time in the storage area). The simulation experiment results demonstrate that the zoning technology implementation according to the Pareto principle at the seaport container terminal (if the vessel has permission according to the preliminary informing technology of the state regulatory authorities) is possible.