Continuous-flow microwave heating has good potential in liquid food processing. Efficiency and uniformity of continuous-flow heating are critical to processing results. During continuous-flow heating, the dielectric constant of the liquid varies with increasing temperature, and the efficiency and uniformity of continuous-flow heating are compromised under significant dynamic variations in the dielectric constant of the liquid. To address these issues, this paper proposes a continuous-flow microwave heating system based on a coaxial inner conductor structure. First, a multiphysics model was developed, the parameter of the continuous-flow heating system is optimised so that the load effectively absorbs electromagnetic waves, and the heating uniformity can be enhanced due to the uniform cross-sectional electric field distribution of TEM mode in the coaxial structure. Second, experiments were performed to validate the proposed model, and the results were in good agreement with the simulation. The heating efficiency under varying dielectric constants (from 10 to 80) and loss angle tangents (from 0.1 to 0.5) of the liquid was above 90%. Then, the proposed system is compared with multimode cavity and system without waveguide coaxial conversion structure, and the proposed system is more efficient for liquid with different dielectric constants. Next, a section of metal bar was added to the center of the glass tube and the influence of the metal bar on heating effect was analysed. With the addition of the metal bar, the efficiency of the system in heating a low-dielectric-constant liquid could be effectively improved, and the heating uniformity could be increased by more than 30%. Finally, the proposed system was applied to heat liquid food and the results indicated that all of liquid food materials' efficiency larger than 90%. The continuous-flow microwave system provides the possibility for large-scale industrial production.