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The present study aims at designing a cold multi-cycle supply chain based on a multi cross-dock system taking into account uncertainty. In the first step, we identified the factors and variables of the model. In the second, by selecting the study period through designing data collection forms and using the documents reviewing methodologies, the raw data required to measure the final indicators were collected and processed in the project model. Then, they were analyzed considering the research topic and using the techniques of genetic algorithm and particle swarm optimization. The primary objective function is minimizing the cost of transportation and warehousing throughout the supply chain, the second minimizing the total operation time and the number of vehicles within the supply chain, and the third maximizing the product freshness time. Also meta-heuristic optimization methods (strongly adjustable) were adopted to deal with the travel time of suburban vehicles. We also provide an example of the performance of optimization models for a small-sized sample. The computational results showed that longer travel time and further distance do not necessarily increase costs. In fact, it is possible to distribute the products with the right number of trucks at an optimal cost at the right time.