Based on the concept of residual bond, a physical model quantitatively describing the relationship between the melt structure and viscosity of metal is established by mathematical deduction, and the microscopic nature of viscosity is considered to be the evolution of the size d of the residual-bond structure of melt. Using this model, the kinematic viscosityies of the magnesium and aluminum melt in a certain region above the melting point are calculated, and the functional relations vMg=3.1710-7+3.0410-7d and vAl=1.6510-7+1.0510-7d are obtained, which accord with the experimental data measured by the method of crucible rotating oscillation damping. This model reveals the microscopic naturs of the micro-inhomogeneity and viscosity of the melt structure from the view of chemical bond, which provides a new way to calculate the viscosity of melt and is of significance for understanding the relationship between microstructure and macroscopic properties of liquid metal.