The anxieties and concerns about health hazards caused by microwave has been growing recently. Previous studies have reported microwave induced structural and functional injuries to brain. However, the biological effects caused by compound microwave were largely unexplored. In this study, we investigated the biological effects on rat's hippocampus after sequentially exposure to 2.8 GHz and 9.3 GHz at average power density of 10 mW/cm. Morris water maze (MWM) navigation tests showed that microwave exposure significantly extended the average escape latency (AEL) at 1d and 3d after exposure, suggesting reduced learning and memory ability. Importantly, compound microwave produced strongest responses at 3 d after exposure. Moreover, microwave also could induce abnormal electroencephalogram (EEG), such as increasing the power of θ wave and δ wave, suggesting brain damage or dysfunction. Histopathological analysis suggested that microwave resulted in obvious structural injuries in hippocampus at 7 d after exposure, and most serious injuries were observed in compound microwave exposed rats. Moreover, disorder of mitochondria and reduced Nissl bodies in hippocampus might contribute to the decrease of cognitive function. However, both the cognitive function and hippocampal structure restored to normal at 28 d after exposure, which might be attributed to self-recovery mechanisms. Gene ontology (GO) and Protein-protein interaction (PPI) analyses of differential expressed genes (DEGs) in peripheral blood suggested that Htt and Bdnf might be potential indicators to predict microwave. In conclusion, compound microwave of 2.8 GHz and 9.3 GHz could elicit reversible structural injuries to hippocampus, which could decrease the cognitive function of rats.