Polydimethylsiloxane (PDMS) membrane in suitable-fluorinated level have excellent pervaporation performance as well as antibiological contamination performance. The pervaporation membranes with different PDMS/fluorosilane mass ratios, the adsorption and dissolution behaviors of acetone molecules on the membrane surface, as well as the diffusion and permeation behaviors in the membranes are studied by all-atom molecular dynamics simulation (AAMDS). The results show that when the mass ratio of PDMS/fluorosilane is 100/20, the surface solubility of acetone is 11.711 (J cm −3 ) 0.5 , and the interfacial interaction is −16897.0415 kcal mol −1 , both of which are the highest. The results of wide-angle X-ray diffraction (WAXD) showed that there are amorphous regions in the membranes suitable for acetone penetration. The maximum chain spacing of the PDMS/fluorosilane(100/20)_membranes is 10.8482 Å, and the free volume fraction (FFV) is 3.03%, both of which are the largest. The change rate of long-term mean square displacement (MSD) in PDMS/fluorosilane(100/20)_Membrane with time is 0.45269. The Young's modulus E, shear modulus G, volume modulus K, and Poisson's ratio 𝝂 of PDMS/fluorosilane(100/20)_Membrane are 0.3249, 0.4061, 0.0492 GPa and -0.5999, respectively. The elasticity of the membrane enhances the diffusion behavior of acetone molecules, and the self-diffusion coefficient of acetone in the membrane is 0.07545 Å 2 ps −1 .