The cut method has been proved to be extremely useful in chemical graph theory. In this paper the cut method is extended to hypergraphs. More precisely, the method is developed for the Wiener index of $k$-uniform partial cube-hypergraphs. The method is applied to cube-hypergraphs and hypertrees. Extensions of the method to hypergraphs arising in chemistry which are not necessary $k$-uniform and/or not necessary linear are also developed.