Wiener index is one of the topological indices which can be used for analyzing intrinsic properties of molecule structure in chemistry. In this paper we evaluate a wiener index of a graph (molecular graph) in two ways: one is new method by using super edge-magic sequence (SEMS) and the other is a different approach for existing method, using Minimal spanning tree at each vertex. By this, we can reduce laborious procedure in existing method by spanning tree algorithms, as many possible. Particularly the studies on wiener index of the molecular graph to analyze the structure of organic molecules like Cyclo alkane, Alkane-n-amine and Alkane-n,n′-diamine through the SEMS have been presented in this paper.