City logistics focuses on optimizing logistics and transport activities in urban areas while considering traffic congestion, environment and energy consumption. With the increase in urban population, the efficiency and effectiveness of the freight deliveries in city areas are becoming more critical. Although all stakeholders share common objectives of transporting goods in the urban area, each stakeholder can have different priorities considering their conditions. This paper is aimed to treat city logistics modeling for Istanbul by using multi-objective linear programming that considers the different objectives of the stakeholders by integrating goal programming and fuzzy Choquet Integral approaches, in a multi-level supply chain for the automotive industry. The objective functions are minimization of total transportation costs, total inventory holding costs, penalty costs for delayed products and emission level in urban area. It is solved by goal programming, and also fuzzy Choquet Integral method is embedded for the third objective function. The application of the model is realized on city logistics for a company in the automotive industry. This proposed model makes selection decisions among the fuel vehicles and electric vehicles in urban freight transport and also calculates the amount of the products that have to be transported between facilities, the amount of the delayed products and the inventory level for main warehouses in each time period. Finally, the results are discussed under different scenarios.