This study investigated the neural mechanisms of brainwave music on sleep quality. Background: Sleep disorders are a common health problem in our society and may result in fatigue, depression, and problems in daytime functioning. Previous studies have shown that brainwave music generated from electroencephalography (EEG) signals could emotionally affect our nervous system and have positive effects on sleep. However, the neural mechanisms of brainwave music on the quality of sleep need to be clarified. Methods: A total of 33 young participants were recruited and randomly divided into three groups. The participants listened to rapid eye movement (REM) brainwave music (Group 1: 13 subjects), slow-wave sleep (SWS) brainwave music (Group 2: 11 subjects), or white noise (WN) (Control Group: 9 subjects) for 20 min before bedtime for 6 days. EEG and other physiological signals were recorded by polysomnography. Results: We found that the sleep efficiency increased in the SWS group but decreased in REM and WN groups. The sleep efficiency in the SWS group was ameliorated [t(10) = −1.943, p = 0.076]. In the EEG power spectral density analysis, the delta power spectral density in the REM group and in the control group increased, while that in the SWS group decreased [F(2,31) = 7.909, p = 0.005]. In the network analysis, the functional connectivity (FC), assessed with Pearson correlation coefficients, showed that the connectivity strength decreased [t(10) = 1.969, p = 0.073] between the left frontal lobe (F3) and left parietal lobe (C3) in the SWS group. In addition, there was a negative correlation between the FC of the left frontal lobe and the left parietal lobe and sleep latency in the SWS group (r = −0.527, p = 0.064). Conclusion: Slow-wave sleep brainwave music may have a positive effect on sleep quality, while REM brainwave music or WN may not have a positive effect. Furthermore, better sleep quality might be caused by a decrease in the power spectral density of the delta band of EEG and an increase in the FC between the left frontal lobe and the left parietal lobe. SWS brainwave music could be a safe and inexpensive method for clinical use if confirmed by more data.