To ensure the mental health and operational safety of on-orbit operators during deep space exploration missions, the underlying mechanisms of the effects of the space station noise and microgravity composite stress environment on operators' emotions are required to be clarified. A resting-state experiment simulating a composite environment of microgravity and noise was conducted. Subjective mood was evaluated using the profile of mood states. Valence-arousal and multiscale entropy indices were extracted from objective electroencephalogram (EEG) data. A partial least squares regression model was established to predict subjective emotional experiences from physiological features. The results indicate that subjective negative emotions are significantly intensified as sound pressure levels increase. Frontal EEG asymmetry is shifted toward the right hemisphere. The medium-to-long-scale complexity of frontal neural activity is significantly decreased. Furthermore, the negative effects of noise are exacerbated by simulated microgravity. Consequently, the noise tolerance threshold of the subjects is shifted earlier to the range of 55 dB to 65 dB. Psychophysiological responses are closely related under the short-term spaceflight noise environment. Changes in emotional valence are identified as a key indicator for predicting the level of individual mood disturbance. An important scientific basis is provided for optimizing acoustic environment design in space stations, developing emotion recognition systems, and realizing real-time monitoring of the psychological states of on-orbit personnel.