During object-relational database physical structure design, problems are caused by three factors: ambiguity of transformations of conceptual model, multiplicity of quality assessment criteria, and a lack of constructive model. In the present study a constructive hierarchical model of physical database structure has been developed. Implementations are used in XML, SQL and Java languages. Multi-criterial structure optimisation method has also been developed. Structure variation space is generated using transformation rule database. Prototype has been implemented within the framework of the research.