The designed automatic feeding system is verified to solve problems of pipe blockage and feed crushing, which is founded frequently during long-distance pipeline transportation of pellet feed in scenes of deep-sea aquaculture. Using the computational fluid dynamics-discrete element method (CFD-DEM), the study is conducted to analyze the feed motion state, mix rate of feed-air, pipeline pressure drop, pipe blockage, and feed collision frequency in process of feed pneumatic conveying. Moreover, simulation accuracy will be verified by experiments. It is shown that feed pellets are accelerated after entering the pipeline, under the drag force of airflow. The average velocity of pellet feeds in the pipeline is 8.5 m/s. Phenomenons of feed crushing and pipeline blockage easily happen in positions such as feed outlets and elbows. In which the mix rate of feed-air and pressure drop are large, collisions occur frequently during feed and feed, feed, and an inner wall of the pipeline. Fluid simulation can be used to guide automatic feeding system design with a simulation accuracy of 94.4% after experimental verification. There are lots of advantages of an automatic feeding system, such as low energy consumption, low probability of pipeline blockage and feed crushing rate, accurate feed measurement, with a feed crushing rate of 0.4%, feed measurement error lower than 1.3%, energy consumption of feed pneumatic conveying of 3.11~6.40 kW·h/t. This study demonstrates that an automatic feeding system is applicable to scenes of deep-sea aquaculture.