Aiming at addressing the problem of low mechanization of filling and transporting citrus seedling pot in China, a new type of seedling pot filling and transporting machine with 120 pots at a time was designed. Based on the study of the flow characteristic of the seedling substrate, key components of the filling and transporting machine, such as blanking mechanism, transmission mechanism, flap mechanism, and steering mechanism were designed. The effects of the opening width of the hopper, the rotating speed of the stirring shaft, the moisture content of the seedling substrate, and the forward speed of the transporting device on the filling effect of seedling pot were studied by the experimental method, and the optimal operation parameters were determined. The prototype tests were repeated 3 times with the best combination of parameters. The running of the prototype was stable. The number of filling bowls was 120, and the average filling time was about 40 s. The machine was in good condition for loading and unloading. The seedling pots were arranged in order. The average filling mass was 1.881kg, which was 0.006kg different from the predicted value, the relative error was 0.32%, and the mass variation coefficient was 2.97%, which was 0.12% different from the predicted value, the relative error is 4.0%. The designed machine can provide a reference for the development and optimization of the citrus substrate filling and transporting machine.