Anxiety is an interactive disorder of the mind and body, characterized by excessive worry about uncertain future events and a dysfunction of the autonomic nervous system. Previous studies have shown that slow, deep breathing can reduce physical tension, and anxiety. Although we know that slow and deep breathing techniques can effectively regulate anxiety and other emotions, the psychological and neurophysiological mechanisms of slow breathing on anxiety have not been systematically explored. In the study, we combined the paced breathing task with the threat uncertainty task for the first time to investigate the role of slow breathing in regulating anxiety. Here we investigated this question, using Spectral analysis and Time-frequency domain of EEG to assess brain activity relating respiratory rate and the mechanism of respiratory rate impact on the anxious. Twenty-seven individuals participated in the experiment, which followed a 2 (respiratory rate: fast breathing, slow breathing) × 2 (certainty: certain, uncertain) within-subjects design. The results of showed that: (1) Slow breathing effectively reduced anxiety, the valence and arousal are lower under the slow breathing. (2) The EEG of fast and slow breathing showed different characteristics. There is an overall increase in power during slow breathing in the delta, theta, alpha and beta bands.(3) The interaction of respiratory rate and certainty were closely related to beta. In the uncertain, beta power decreased with slow breathing but increased with fast breathing.