Establish the naval battle transportation model based on stochastic delay and fuzzy loss in naval battle transportation, on the basis of it, the genetic algorithm is given based on random simulation. The genetic algorithm takes random number coding, the way of coding with stochastic numbers, dominant genes and concealed genes all taking part in crossover and mutation can reinforce the ability of gain the global optimization solution. Taking naval battle transportation network diagram as example, and some data is given as the example. The result shows that the algorithm is reasonable and efficient, which is valuable for decision-making of naval battle transportation route.