The Ebola virus is a highly infectious and rare virus. In order to control the further spread of the Ebola virus, make the vaccine efficiently and quickly transport to the hardest hit by the disease, reduce constantly the number and scale of the Ebola epidemic, and ultimately control the spread of the virus, we use the shortest path to solve this problem. First, the model of shortest path problem is established. Then the polymorphic ant colony algorithm is applied to accomplish shortest path problem. Finally, it is showed in the simulation experiments that the PACA can reasonable to solve shortest path problem in Ebola virus prorogation, and it has a great advantage in search time, convergence speed, and optimization result and algorithm efficiency.