Aiming at fleet deployment issue and cargo allocation issue under the background of COVID19 epidemic and the “dual carbon” strategy, in order to meet the requirements of liner companies for the balanced development of fleet transportation efficiency, economic benefits, service quality and environmental benefits, a multiobjective fleet deployment and cargo allocation optimization model was established to achieve the goal of maximizing fleet average space utilization and operating profit, minimizing cargo time value loss and single container carbon emission. According to the internal relationship between subproblems, the model was decomposed into a twolevel model. The upper level was mixed integer nonlinear programming to deal with route ship allocation and speed optimization, and the lower level was linear programming to deal with cargo allocation. The solution algorithm was designed based on NSGAⅡ algorithm framework. Taking the fleet of a liner company as example, the results show that the model and the optimization solution method are feasible, and the liner company can adopt the mixed strategy of slightly increasing the speed and increasing the number of small and mediumsized ships to achieve the effect of carbon emission reduction while meeting more freight demand and coping with port congestion.