In iron-containing silicate melts such as gasification slags and geological slags, iron can play a different role in the melt properties because of its varying valence states. In this paper, the structural characteristics and viscosities of five samples were studied by molecular dynamics simulation and thermodynamic calculation methods. The effect of different iron species on the structure and properties is revealed. More than half of the Fe3+ ions are in four-coordination. The four- and fivefold coordinated ferric ions are in dynamic equilibrium. The four-coordinated Fe3+ can connect with the other tetrahedrons centered by Si4+ and Al3+ or integrate into three-coordinated oxygen units. With an increase of the iron content, the polymerization degree characterized by nonbridged oxygen per tetrahedra (NBO/T) is found to be inconsistent with the trend of viscosity. Based on the energy of the different types of oxygen, a new parameter RStotal is proposed to substitute the original NBO/T and correlate with viscosity in an exponential function. Liquid iron can form in molten slags under a strong reducing atmosphere, which can inhibit the diffusion of oxygen and increase the viscosity.