A multi-layer tray-type hot air-assisted microwave drying machine was designed to address the issues of non-uniform airflow and electromagnetic field distribution, low drying efficiency, and poor drying quality during static drying of existing straw-based nutrient seedling-growing bowl tray (referred to as seedling trays). The microwave resonant cavity and airflow distribution chamber of the drying machine were optimized. ANSYS Electronics software was used to simulate different arrangements of the microwave resonant cavity feed ports, based on the uniformity of electromagnetic field intensity and the influence of S-parameters, to determine the arrangement and height of the feed ports. ANSYS Fluent software was used to optimize the height of deflector chamber and height of airflow distribution chamber, as well as diameter of the bottom edge of deflector. The performance and heating uniformity of the machine were experimentally verified by using the seedling tray as the test material. The results showed that the uniformity index of gas velocity at the outlet of the optimized airflow distribution chamber was increased by 21.26% compared with that before optimization. The V-L-L arrangement of the three feed ports in the microwave resonant cavity had the best electromagnetic field intensity uniformity and the smallest S-parameters.The reflectivity was the lowest when the feed port height was 160mm, decreasing by 78.13% compared with height of 70mm. Compared with hot air drying and microwave drying, the drying rate of the seedling tray under hot air-assisted microwave drying was increased by 291.31% and 86.48%, respectively, and the drying uniformity was better. The research result can provide a reference for the structural optimization of hot air-assisted microwave drying machines.