Powder-bed electron beam additive manufacturing has the potential to be a cost-effective alternative in producing complex-shaped, custom-designed metal parts using various alloys. Material thermal properties have a rather sophisticated effect on the thermal characteristics such as the melt pool geometry in fabrications, impacting the build part quality. The objective of this study is to achieve a quantitative relationship that can correlate the material thermal properties and the melt pool geometric characteristics in the electron beam additive manufacturing process. The motivation is to understand the interactions of material property effect since testing individual properties is insufficient because of the change of almost all thermal properties when switching from one to the other material. In this research, a full-factorial simulation experiment was conducted to include a wide range of the thermal properties and their combinations. A developed finite element thermal model was applied to perform electron beam additive manufacturing process thermal simulations incorporating tested thermal properties. The analysis of variance method was utilized to evaluate different thermal property effects on the simulated melt pool geometry. The major results are summarized as follows. (1) The material melting point is the most dominant factor to the melt pool size. (2) The role of the material thermal conductivity may outweigh the melting point and strongly affects the melt pool size, if the thermal conductivity is very high. (3) Regression equations to correlate the material properties and the melt pool dimension and shape have been established, and the regression-predicted results show a reasonable agreement with the simulation results for tested real-world materials. However, errors still exist for materials with a small melt pool such as copper.