Vinyl Benzoate/Heptadecafluorodecyl acrylate (VBe/HFDA) co-polymers were synthesized and characterized as thickening agents for supercritical carbon dioxide (SC-CO2). The solubility and thickening capability of the co-polymer samples in SC-CO2 were evaluated by measuring cloud point pressure and relative viscosity. The molecular dynamics (MD) simulation for all atoms was employed to simulate the microscopic molecular behavior and the intermolecular interaction of co-polymer–CO2 systems. We found that the introduction of VBe group decreased the polymer–CO2 interaction and increased the polymer–polymer interaction, leading to a reduction in solubility of the co-polymers in SC-CO2. However, the co-polymer could generate more effective inter-chain interaction and generate more viscosity enhancement compared to the Poly(Heptadecafluorodecyl) (PHFDA) homopolymer due to the driving force provided by π-π stacking of the VBe groups. The optimum molar ratio value for VBe in co-polymers for the viscosity enhancement of SC-CO2 was found to be 0.33 in this work. The P(HFDA0.67-co-VBe0.33) was able to enhance the viscosity of SC-CO2 by 438 times at 5 wt. %. Less VBe content would result in a lack of intermolecular interaction, although excessive VBe content would generate more intramolecular π-π stacking and less intermolecular π-π stacking. Both conditions reduce the thickening capability of the P(HFDA-co-VBe) co-polymer. This work presented the relationship between structure and performance of the co-polymers in SC-CO2 by combining experiment and molecular simulations.