In this work, hollow truss structures with different internal microstructure distributions, i.e., basic hollow truss structure (specimen HT), hollow truss structure with internal microstructure at joints (specimen HTSJ), and hollow truss structure with internal microstructure on tube walls (specimen HTSW), were designed and manufactured using a selective laser melting technique. The effect of internal microstructure distribution on quasi-static compressive behavior and energy absorption was investigated by experimental tests and numerical simulations. The experimental results show that compressive strength and specific compressive strength of specimen HTSW increase by nearly 50% and 14% compared to specimen HT, and its energy absorption per volume and mass also increase by 52% and 15% at a strain of 0.5, respectively. However, the parameters of specimen HTSJ exhibit limited improvement or even a decrease in different degrees in comparison to specimen HT. The numerical simulation indicates that internal microstructures change the bearing capacity and structural weaknesses of the cells, resulting in the different mechanical properties and energy absorptions of the specimens. Based on the internal microstructure design in this study, adding microstructures into the internal weaknesses of the cells parallel to the loading direction is an effective way to improve the compressive properties, energy absorption and compressive stability of hollow truss structures.