Separation process is one of the key processes in the production of fruit spirits, including the traditional distillation method and the new pervaporation membrane method. The separation process significantly determines the constituents and proportions of compounds in the fruit spirit, which has a significant impact on the spirit quality and consumer acceptance. Therefore, it is important and complex to reveal the changing rules of chemical substances and the principles behind them during the separation process of fruit spirits. This review summarized the traditional separation methods commonly used in fruit spirits, covering the types, principles, and corresponding equipment of distillation methods, focused on the enrichment or removal of aroma compounds and harmful factors in fruit spirits by distillation methods, and tried to explain the mechanism behind it. It also proposed a new separation technology for the production of fruit spirits, pervaporation membrane technology, summarized its working principle, operation, working parameters, and application in the production of fruit spirits, and outlined the impact of the separation method on the production of fruit spirits based on existing research, focusing on the separation of flavor compounds, sensory qualities, and hazard factors in fruit spirits, along with a preliminary comparison with distillation. Finally, according to the current researches of the separation methods and the development requirement of the separation process of fruit spirits, the prospect of corresponding research is put forward, in order to propose new ideas and development directions for the research in this field.