The spinel oxide AlV₂O₄is a unique material, in which the formation of clusters is accompanied by atomic, charge and orbital ordering and a rhombohedral lattice distortion. In this work a theory of the structural phase transition in AlV₂O₄is proposed. This theory is based on the study of the order-parameter symmetry, thermodynamics, electron density distribution, crystal chemistry and mechanisms of formation of the atomic and orbital structures of the rhombohedral phase. It is established that the critical order parameter is transformed according to irreducible representationk₉(τ₄) (in Kovalev notation) of the Fd \bar{3}m space group. Knowledge of the order-parameter symmetry allows us to show that the derived AlV₂O₄rhombohedral structure is a result of displacements of all atom types and the ordering of Al atoms (1:1 order type in tetrahedral spinel sites), V atoms (1:1:6 order type in octahedral sites) and O atoms (1:1:3:3 order type), and the ordering ofd_xy,d_xzandd_yzorbitals. Application of the density functional theory showed that V atoms in the Kagomé sublattice formed separate trimers. Also, no sign of metallic bonding between separate vanadium trimers in the heptamer structure was found. The density functional theory study and the crystal chemical analysis of V—O bond lengths allowed us to assume the existence of dimers and trimers as main clusters in the structure of the AlV₂O₄rhombohedral modification. The trimer model of the low-symmetry AlV₂O₄structure is proposed. Within the Landau theory of phase transitions, typical diagrams of possible phase states are built. It is shown that phase states can be changed as a first-order phase transition close to the second order in the vicinity of tricritical points of the phase diagrams.