Vanadium-based kagomé systems AV3Sb5 (A = K, Rb, Cs) have emerged as paradigmatic examples exhibiting unconventional charge density waves (CDWs) and superconductivity linked to van Hove singularities (VHSs). Despite extensive studies, the three-dimensional (3D) nature of CDW states in these systems remains elusive. This study employs first-principles density functional theory and a tight-binding model to investigate the stacking-dependent electronic structures of 3D CDWs in AV3Sb5, emphasizing the significant role of interlayer coupling in behaviors of the VHSs associated with diverse 3D CDW orders. We develop a minimal 3D tight-binding model and present a detailed analysis of band structures and density of states for various 3D CDW stacking configurations, including those with and without a π-phase shift stacking of the inverse star of David, as well as alternating stacking of the inverse star of David and the star of David. We find that VHSs exist below the Fermi level even in 3D CDWs without π-phase shift stackings, and that these VHSs shift downward in the π-phase shift stacking CDW structure, stabilizing the 2×2×2π-shifted inverse star of David distortions in alternating vanadium layers as the ground state 3D CDW order of AV3Sb5. Our work provides the electronic origin of 3D CDW orders, paving the way for a deeper understanding of CDWs and superconductivity in AV3Sb5 kagomé metals.