Since the outbreak of COVID-19, a large number of passengers infected on multiple cruise ships have exposed the shortcomings of existing ship design methods in epidemic prevention functions. This paper proposes a risk analysis method based on people flow simulation to address the risk of infectious diseases caused by flow of people on board. The internal spatial characteristics and people flow simulation model of a ship with medical function are constructed in the current study. The people flow under specified operation conditions is then simulated based on the cellular automata method. The risk level of various places within the ship’s space are obtained by combining with the infection probability model of a specific virus strain. The analysis results show that the overall layout design of the target ship based on the principle of zoning management can control the risk of infection transmission to a certain extent, but it is still necessary to further optimize the details of the cabin passage layout and daily management. The analysis methods and examples used in the current study can provide references for the epidemic prevention design of the general arrangement of ships and give suggestions for the management of the onboard people flow under the epidemic situation.