Structural components and characteristics of WDG-5 type microwave freeze dryer were introduced, and the causes of uneven drying were analyzed. The experiments about the influence of microwave control methods on the drying uniformity were conducted on this dryer using the material of carrot. The results concluded that out layers of 20 material plates were dried faster than inner ones. Compared with the whole working method of microwave system, the two-group alternative working method evidently improved the drying uniformity among plate layers. As for the materials within the same layer plate, peripheral materials were dried faster than central ones. And the drying uniformity of the same plate materials was also improved greatly under the two-group alternative working method of microwave system in contrast with the whole working method.