In this paper, three sorts of network indices for the weighted three-layered graph are studied through the methods of graph spectra theory combined with analysis methods. The concept of union of graphs are applied to design two sorts of weighted layered multi-fan composed graphs, and the accurate mathematical expressions of the network indices are obtained through the derivations of Laplacian spectra; furthermore, the asymptotic properties are also derived. We find that when the cardinalities of the vertices on a sector-edge-link tend to infinity, the indices of FONC and EMFPT are irrelevant with the number of copies of the fan-substructure based on the considered graph framework.