The COVID-19 pandemic first broke out in 2020 and rapidly spread globally, which had a great impact on shipping companies, ports and cargo owners. Many nations have closed their ports and raised quarantine requirements, leading to frequent incidents of ship skipping and ship stoppages. Although the COVID-19 pandemic has been brought under control, similar or more serious public health events may still occur in the future worldwide, which will have a greater impact on ship transportation. This study focuses on optimizing the route and speed of container ships in the pandemic environment by constructing a mixed integer programming model, which provides better response strategies for ship operators. Existing studies have reported that the pandemic has significantly impacted international ships’ ocean-going routes, resulting in an increase in the total cost of ship operations on the routes. Moreover, ships that on ocean going routes were less affected by the pandemic, and generally can cope well with the pandemic after speed optimization; while ships on near-ocean routes are more susceptible to the pandemic, and are more likely to optimize costs by choosing a port-hopping strategy. The study also found that the choice of ship routes is affected by factors (e.g., the number of containers loaded and unloaded, the distance between the strictly controlled port and the next port, and the range of port quarantine period). Fuel prices have no significant impact on the choice of ship routes.