Auxetic materials, a novel category with a negative Poisson’s ratio, demonstrate enhanced mechanical performance over the conventional materials. This study specifically explores the influence of joint shapes and sizes on the mechanical properties of auxetic re-entrant structures, focusing on Young’s Modulus, peak stress, and energy absorption capabilities. A numerical model was developed and validated through experimental comparisons. Four joint shapes—Circle, Square, Equilateral triangle, and Rhombus—were examined for their impact on the mechanical performance of auxetic re-entrant structures. The structures with various joint shapes were 3D printed using an FDM 3D printer, and their in-plane mechanical properties were assessed. Results indicated that the circular joint exhibited the highest Young’s modulus, while the rhombus joint displayed the highest peak stress and energy absorption capability. Additionally, a parametric investigation into the size impact of different joint shapes on auxetic re-entrant structure performance was conducted using the numerical model. In summary, the results emphasize the considerable impact of both joint shape and size on the mechanical properties of auxetic re-entrant structures.