Tobacco smoking is the leading preventable cause of morbidity and mortality worldwide. Although a number of smokers are aware of the adverse outcomes of smoking and express a strong desire to stop smoking, most smoking quit attempts end in relapse within the first few days of abstinence, primarily resulting from the aversive aspects of the nicotine withdrawal syndrome. Therefore, studying the neural mechanisms of smoking abstinence, identifying smokers with heightened relapse vulnerability prior to quit attempts, and developing effective smoking cessation treatments appear to be promising strategies for improving the success of quit attempts. In recent years, with the development of magnetic resonance imaging, the neural substrates of smoking abstinence have become extensively studied. In this review, we first introduce the psychophysiological changes induced by smoking abstinence, including affective, cognitive, and somatic signs. We then provide an overview of the magnetic resonance imaging-based evidence regarding abstinence-related functional changes accompanied by these psychophysiological changes. We conclude with a discussion of the neural markers that could predict relapse during quit attempts and a summary of the psychophysiological interventions that are currently often used to help with smoking cessation. This review extends our understanding of the role of the central nervous system in smoking abstinence.