Microwave ablation can produce immune activation due to thermal effects. However, the nonthermal effects of microwaves on the immune system are still largely unexplored. In this study, we sequentially exposed rats to 1.5 GHz microwave for 6 min and 2.8 GHz microwave for 6 min at an average power density of 5, 10, and 30 mW/cm2. The structure of the thymus, spleen, and mesenteric lymph node were observed, and we showed that multifrequency microwave exposure caused tissue injuries, such as congestion and nuclear fragmentation in lymphocytes. Ultrastructural injuries, including mitochondrial swelling, mitochondrial cristae rupture, and mitochondrial cavitation, were observed, especially in the 30 mW/cm2 microwave-exposed group. Generally, multifrequency microwaves decreased white blood cells, as well as lymphocytes, monocytes, and neutrophils, in peripheral blood, from 7 d to 28 d after exposure. Microwaves with an average density of 30 mW/cm2 produced much more significant inhibitory effects on immune cells. Moreover, multifrequency microwaves at 10 and 30 mW/cm2, but not 5 mW/cm2, reduced the serum levels of several cytokines, such as interleukin-1 alpha (IL-1α), IL-1β, interferon γ (IFN-γ) and tumor necrosis factor α (TNF-α), at 7 d and 14 d after exposure. We also found similar alterations in immunoglobulins (Igs), IgG, and IgM in serum. However, no obvious changes in complement proteins were detected. In conclusion, multifrequency microwave exposure of 1.5 GHz and 2.8 GHz caused both structural injuries of immune tissues and functional impairment in immune cells. Therefore, it will be necessary to develop an effective strategy to protect people from multifrequency microwave-induced immune suppression.