In this work, n-hexane, cyclohexane and 2-methylpentane were selected to represent linear-alkane, cycloalkane and branched-alkane, respectively. Based on the dynamic light method (DLS), the viscosity, interfacial tension and diffusion coefficient of n-hexane/CO2, cyclohexane/CO2 and 2-methylpentane/CO2 systems under saturation condition were measured in order to explore the change trend of thermophysical properties of the systems with the same carbon atom number but different molecular structures. The experiments were conducted at the temperatures of 303, 343 and 383 K and at pressures up to 5.64 MPa. The expanded uncertainties(k = 2)of dynamic viscosity, interfacial tension and diffusion coefficient were 3 %, 3 % and 4.4 % respectively. The experimental results show that n-hexane and 2-methylpentane with similar molecular structure have more similar value of the properties. The effects of different alkane structures on system viscosity, interfacial tension, and diffusion coefficient were explained at the molecular level through radial distribution function, interface thickness, and CO2 coordination number. At 303.15 K and 4 MPa, the peak radial distribution function of CO2/cyclohexane is 1.845, which is greater than that of CO2/n-hexane and CO2/2-methylpentane molecules. It has been proven that the arrangement of CO2/cyclohexane is more orderly, resulting in higher viscosity and lower diffusion coefficient of the system. The interface thickness of CO2/cyclohexane is 6.13 nm, which is smaller than CO2/n-hexane (7.53 nm) and CO2/2-methylpentane (6.3 nm). The smaller the interface thickness, the more compact the structure, the stronger the intermolecular forces, and the greater the interfacial tension. At 303.15 K and 2 MPa, the number of CO2 coordination sites within 1 nm around liquid phase alkanes is 3.96, which is smaller than 4.78 for cyclohexane and 6.62 for 2-methylpentane. Prove that the coordination number is directly proportional to the diffusion coefficient and inversely proportional to viscosity and interfacial tension.