In response to the changes in environmental temperature and humidity, as well as the phenomenon of soybean seed respiration causing topping and clumping in the seed storage room, which leads to problems such as mold or germination during seed storage, the work aims to design a low temperature drying and storage system for agricultural products based on a heat pump system for soybean breeding samples. The load of each component was calculated through mathematical models. Appropriate airflow organization forms were selected according to CFD simulation technology results. Then an experimental analysis on the stability of the designed system's supply air temperature and humidity, the uniformity of indoor supply air, and the temperature uniformity was conducted. A system based on single side air supply and opposite side return air flow organization was designed. During the drying, the temperature fluctuation range of the air supply was ±1 ℃, the humidity fluctuation range was ± 4% RH, the maximum indoor temperature deviation was 1.8 ℃, and the indoor air supply speed was less than 2 m/s. The conclusion is based on reasonable selection design calculation and air supply organization layout. This design provides an ideal environment for the long-term storage of breeding samples. The uniform temperature field and airflow distribution not only effectively reduce the cost of manual storage, but also ensure the storage quality of samples. This design can provide reliable support for breeding research and have a positive impact on agricultural development.