Lotus root planting has a long history in China, more than 3000 years ago. The lotus root harvesting machines suitable for the Yellow River Delta region is still in the design optimization stage. This paper provides a method based on the Fluent-EDEM simulation to design the jet system of the lotus root harvesting machine, solve the problems of low lotus root harvesting rate and high lotus root damage rate, and improve the efficiency of lotus root harvesting. Using Fluent-EDEM coupled simulation software, single factor tests were carried out to study the influence of jet angle, jet velocity, and nozzle height on picking time. A regression model was established through orthogonal tests, and the interaction between various factors was analyzed by using variance analysis. The response surface was used to solve the optimal parameter combination of each factor. The optimal results were obtained as follows: the jet angle was 64.42°, the jet velocity was 30 m/s, the nozzle height was 10 mm. According to the simulation results, the pressure of the jet system was analysed to avoid damage the lotus roots because of excessive pressure.