The cell ultrastructural images of different parts of flue-cured tobacco were quantified by digital quantitative image method, the relationship between cell area, cell perimeter, cell shape factor, vacuole area, cell wall thickness, ratio of vacuole area to cell area and chemical composition index of flue-cured tobacco quality was analyzed. The results showed that the cell outline on the surface of flue-cured tobacco leaves was clear, there were obviously cell nucleus, chloroplast, mitochondria and other adherent distribution on the inner side of cell wall, and the central large vacuole filled the cells in the middle. The cell area, vacuole area and cell perimeter in the upper leaves of flue-cured tobacco were small, and the cell wall thickness was large; the cell area, vacuole area, cell perimeter and cell wall thickness in the middle leaves were small; the vacuole area, cell wall thickness and the ratio of vacuole area to cell area in the lower leaves was large. The thickness of cell wall is positively correlated with the contents of protein and chlorine, and negatively correlated with the content of total sugar; the cell area, cell perimeter, and cell shape factor are positively correlated with the contents of nicotine and total nitrogen; the cell area, vacuole area are positively correlated with the content of reducing sugar; the cell shape factor and the ratio of vacuole area to cell area are negatively correlated with protein content.