In arXiv:1709.07504 Ardila and Aguiar give a Hopf monoid structure on hypergraphs as well as a general construction of polynomial invariants on Hopf monoids. Using these results, we define in this paper a new polynomial invariant on hypergraphs. We give a combinatorial interpretation of this invariant on negative integers which leads to a reciprocity theorem on hypergraphs. Finally, we use this invariant to recover well-known invariants on other combinatorial objects (graphs, simplicial complexes, building sets etc) as well as the associated reciprocity theorems.