Automatic emotion regulation (AER) is an important type of emotion regulation in our daily life. Most of the previous studies concerning AER are done in the conscious level. Little is known about the AER under the subliminal level. The present study was to investigate the AER at the different perceptual levels (i.e., explicitly and implicitly) simultaneously, and the associated neural differences using functional magnetic resonance imaging. Priming paradigm was adopted in which the inhibition or neutral words were used as primes and the negative picutres were used as targets. In the experiment, the duration time of priming words was manipulated at 33 or 50 ms in the implicit level and 3000 ms in the explicit level. The participants were required to make emotional valence rating of the negative pictures while undergoing functional magnetic resonance imaging scanning. The results showed that the participants experienced less negative emotion in inhibition words priming condition contrary to neutral words priming condition. Significant differences were also found in the left ventrolateral prefrontal cortex and left dorsolateral prefrontal cortex at the implicit and explicit AER. The findings of this study demonstrate that inhibition words can automatically and effectively reduce an individual's negative emotion experience, and left ventrolateral prefrontal cortex and left dorsolateral prefrontal cortex have been both implicated in self-control during AER.