Previous studies have explored resting‐state functional connectivity (rs‐FC) of the amygdala in patients with autism spectrum disorder (ASD). However, it remains unclear whether there are frequency‐specific FC alterations of the amygdala in ASD and whether FC in specific frequency bands can be used to distinguish patients with ASD from typical controls (TCs). Data from 306 patients with ASD and 314 age‐matched and sex‐matched TCs were collected from 28 sites in the Autism Brain Imaging Data Exchange database. The bilateral amygdala, defined as the seed regions, was used to perform seed‐based FC analyses in the conventional, slow‐5, and slow‐4 frequency bands at each site. Image‐based meta‐analyses were used to obtain consistent brain regions across 28 sites in the three frequency bands. By combining generative adversarial networks and deep neural networks, a deep learning approach was applied to distinguish patients with ASD from TCs. The meta‐analysis results showed frequency band specificity of FC in ASD, which was reflected in the slow‐5 frequency band instead of the conventional and slow‐4 frequency bands. The deep learning results showed that, compared with the conventional and slow‐4 frequency bands, the slow‐5 frequency band exhibited a higher accuracy of 74.73%, precision of 74.58%, recall of 75.05%, and area under the curve of 0.811 to distinguish patients with ASD from TCs. These findings may help us to understand the pathological mechanisms of ASD and provide preliminary guidance for the clinical diagnosis of ASD.