Objectives: The objective of this study was to explore the effects of short-term mindfulness training on the emotional state of individuals with different levels of mindfulness, especially from the perspective of autonomic neurophysiological mechanism. Methods: 52 college students were divided into higher or lower dispositional mindfulness groups. Then they underwent the measurement periods of baseline, short-term mindfulness training and recovery. During these periods, wrist-worn wearable devices were used for recording their autonomic nervous system activities, including heart rate (HR), galvanic skin response (GSR) and pulse rate variability (PRV). The Positive and Negative affect Scale (PANAS) and the State Anxiety Inventory (S-AI) were used before and after the experiment. Results: The results showed that in both groups, instead of positive emotion, negative emotions and state anxiety reduced significantly after the training. In terms of physiological signals, in lower-dispositional group, the HR of the recovery period were significantly lower than that of the other two periods, and the PRV of the recovery period were significantly higher. In higher-dispositional group, the GSR of recovery period was significantly higher than that of the other two periods. Conclusions: The results suggest that short-term mindfulness training works mainly by reducing negative emotions rather than increasing positive ones. Our findings also provide neurophysiological evidence for a better emotional intervention effect of short-term mindfulness training on individuals with lower dispositional mindfulness.