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An economic criterion called as yearly net profit of single separating unit (YNPSSU) was presented to evaluate the influence of structure optimization on the economy. Using YNPSSU as a criterion, economic analysis was carried out for the structure optimization of separating unit in the case of separating SiF4 to obtain the 28Si and 29Si isotope. YNPSSU was calculated and compared with that before optimization. The results showed that YNPSSU was increased by 12.3% by the structure optimization. Therefore, the structure optimization could increase the economy of the stable isotope separation effectively.