Graph theory has numerous application to problems in systems analysis, operations research, economics, and transportation. However, in many cases, some aspects of a graph-theoretic problem may be uncertain. For example, the vehicle travel time or vehicle capacity on a road network may not be known exactly. In such cases, it is natural to deal with the uncertainty using the methods of fuzzy sets and fuzzy logic. Hypergraphs (Berge,1989) are the generalization of graphs in case of set of multiarity relations. It means the expansion of graph models for the modeling complex systems. In case of modelling systems with fuzzy binary and multiarity relations between objects, transition to fuzzy hypergraphs, which combine advantages both fuzzy and graph models, is more natural. It allows to realise formal optimisation and logical procedures. However, using of the fuzzy graphs and hypergraphs as the models of various systems (social, economic systems, communication networks and others) leads to difficulties. The graph isomorphic transformations are reduced to redefinition of vertices and edges. This redefinition doesn’t change properties the graph determined by an adjacent and an incidence of its vertices and edges. Fuzzy independent set, domination fuzzy set, fuzzy chromatic set are invariants concerning the isomorphism transformations of the fuzzy graphs and fuzzy hypergraph and allow make theirs structural analysis.