Currently, the world’s ever presented changes and the epidemic of COVID are intertwined, and the world economy is struggling to recover. Accelerating the construction of a national unified market is an important basis for China’s economic development to achieve long-term and overall goals. As an important part of China’s economy, the business performance of the tobacco industry is closely related to the logistics management and service levels of tobacco commercial enterprises. In the context of the general implementation of lean logistics management in tobacco commercial enterprises, this paper determines the index set for evaluating the performance of lean logistics in tobacco commercial enterprises through literature research and field studies, uses questionnaires and expert research methods to improve the index set, and completes the evaluation of the importance of the indexes. The indicators are classified and stratified based on factor analysis, so as to build an evaluation index system for the lean logistics performance of tobacco commercial enterprises, lay the evaluation foundation for the high-quality development of the tobacco industry, and promote the construction of a national unified market.