Using density functional theory calculations we study atomic, electronic, and magnetic structures and their influence on the topological phase of Mn2Bi2Te5 and Mn2Sb2Te5 van der Waals compounds. Our results show that the antiferromagnetic topological insulator (AFM TI) phase in Mn2Bi2Te5 is robust both to details of the magnetic ordering within its structural units, nonuple layer (NL) blocks, and the type of atomic layer stacking, NaCl-Type ABC or NiAs-Type ABAC, within the (MnTe)2 sublattice. The structure with the NiAs-Type stacking is energetically more favorable for both compounds. However, for Mn2Sb2Te5 the AFM TI phase is realized in the unstable structure with ABC stacking while it is a Dirac semimetal in favorable structure with NiAs stacking within a (MnTe)2 sublattice. We also show that imposing the overall ferromagnetic state by applying an external magnetic field can drive the Mn2Bi(Sb)2Te5 compounds into different topologically nontrivial phases like axion insulator or Weyl semimetal.