A finite element model (FEM) using a more realistic three-dimensional geometry of lattice truss core was proposed to simulate the flatwise compression test on lattice truss core sandwich composites (LTCSCs). The goal was to reduce the disparity between experimental results and FEM predictions without inclusion of imperfection, as oppose to similar studies. Besides, two modified Kagome topologies were suggested and fabricated by adding vertical composite struts at specific locations. Based on the experimental results, the modified Kagome topologies exhibited superior specific compressive stiffness and strength over the Kagome topology, by about 100%. In addition, facesheet rotation of Kagome topology was found by the FEM, which considerably affect its compressive performance. Facesheet rotation is caused by the arrangement of composite struts of LTCSC. Compressive response of LTCSC was acceptably predicted by the FEM, though there was quite high error for compressive stiffness and strength. Probable sources of discrepancy between experimental and FEM results were discussed.