Abstract: To clarify the structure-property relationships between the three-dimensional structure of filter membranes to achieve the targeted refinement of tobacco extracts, the structural changes of typical filter membranes before and after tobacco filtration were quantitatively examined and calculated. By combining the analysis of the active components in the tobacco extracts, the microstructure of the filter membranes and their mechanisms of separation and refinement of tobacco extracts were dissected. Dynamic light scattering (DLS) and gas chromatography-mass spectrometry (GC-MS) analyses were used to characterize the changes in particle sizes and components of the tobacco extracts before and after membrane separation. High-resolution CT scanning technique was used for structural characterization of the filter membranes. In addition, the deep learning technique was combined with the U-Net neural network algorithm to quantitatively calculate the structural parameters of the filter membranes. The results showed that: 1) Compared with PA membrane, PTFE membrane could retain more solid phase materials and nicotine from tobacco extracts. 2) The calculations by intelligent segmentation showed that the porosity of PA membrane decreased by 4.4%, the thickness increased by 0.6 mm, and the average fiber diameter decreased by 154.73 μm after filtration, which was caused by membrane fiber squeezing due to membrane pore blockage. 3) The PTFE membrane with a pore size of 0.22 μm had an average fiber diameter of 1 694.0 μm and a porosity of 42.7%, which were smaller than those of the PA membrane. The dense fiber alignment of the PTFE membrane resulted in greater retention of solid phase materials. A quantitative method to analyze the three-dimensional structure of the filter membranes was proposed by integrating the microstructural characterization of the filter membrane with deep learning and correlating it with the component changes in the extract sample before and after filtration, which provided a theoretical reference for targeted filter separation of tobacco extracts.