The diffusion of five flavor organic molecules, including D-limonene, myrcene, ethyl hexanoate, 2-nonanone, and linalool in low density polyethylene (LDPE) film were investigated by combined experimental and molecular dynamics (MD) simulation studies. The diffusion coefficients derived from the prediction model, experimental determination, and MD simulation were compared, and the related microscopic diffusion mechanism was investigated. The effects of the presence of the flavor organic molecules on the diffusion of O2 and H2O in polyethylene (PE) were also studied by MD simulation. Results show that: The diffusion of five flavor molecules in LDPE is well followed to Fick’s second law by the immersion experiment; MD simulation indicates the dual mode diffusion mechanism of the flavor molecules is in LDPE; the diffusion coefficients from MD simulation are close to those from the experimental determination, but are slightly larger than those values; the presence of the flavor organic molecules hinders the diffusion of O2 and H2O, which can be well explained from the fraction of free volume (FFV) and interaction energy calculation results derived from MD simulation.