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There are a number of potential health risks associated with prolonged or high-intensity exposure to microwave radiation. However, the biological effects of microwave radiation on the body and related mechanisms have not been elucidated. Uncovering the effects of microwave radiation on non-human primates (NHPs) holds immense value in translating findings cross-species into human studies. The NHP paired associative (PAL) learning paradigm was established. Subsequently, 5 macaques were subjected to low-dose microwave exposure (15 min per day, continuously exposed for 5 days). PAL tests were conducted before and after exposure to assess the effects of microwave radiation on cognitive behavior in macaque monkeys. Electroencephalograms (EEGs) were recorded before exposure, during exposure, immediately, 3d, 7d, 14d, and 28d after exposure to assess the changes of brain function by microwave radiation. The results showed that macaques had no positional preference, no color preference, no left-right handedness preference, and learned the PAL task. The changes of behavioral indexes after microwave radiation showed that microwave radiation interfered with execution ability .and slowed down the process of spontaneous forgetting in macaques. EEG results showed that with prolonged exposure, the macaques experienced a brief EEG recovery after the initial cumulative exposure disturbance. In addition, EEG activity in different brain regions of macaques was disturbed during microwave exposure, and the frequency band of EEG disturbance in some brain regions changed, especially the prefrontal and frontal regions, after microwave exposure relative to the frequency band during exposure. Microwave radiation interfered with executive abilities and resting-state EEG in macaques.