The dissertation has developed and described the dynamic model of ship's refrigeration system with controlled atmosphere, which enables the simulation of its dynamic behaviour. The method of System Dynamics and Powersim simulation programme have been used for modelling. Taking into consideration the fact that ship's refrigerated system with controlled atmosphere is a complex dynamic system, it has been studied and analysed through simpler subsystems which have been created on the key components. Special mathematical models of specific subsystems have been developed in the following way: ship's hold wall, refrigerated humid air in the hold, refrigerated cargo, equipment of ship's refrigerated hold, air cooler, fan of air cooler, brine system, evaporator of brine chiller and its condensation unit, and then the models of: gas exchange by respiration of fruit and vegetables, heat loads by respiration, moisture release by transpiration and CA device. The mathematical models, with concentrated parameters, have been based on the balances of masses, energy and the quantity of movement. Special physical and geometric data as well as experimental results obtained on refrigerated system of a conventional refrigerated vessel "Lady Račišće" have been used for production of simulation model and testing its validity. By means of computer simulation, the results have been achieved which enable practical analysis of dynamic behaviour of the system analysed i.e. the analysis of the air condition in the hold, changes of the temperature of the refrigerated cargo and analysis of the interaction of individual parameters. Dynamic model of the total system has been verified by means of the comparison of the simulation results with existing experimental results, being of considerable correspondence. The thesis has also given an exhaustive survey of recent published research in the area, the description of the CA technology and its influence on the physiological processes of fruits and vegetables.