An $r$-uniform supertree is a connected and acyclic hypergraph of which each edge has $r$ vertices, where $r\geq 3$. We propose the concept of matching energy for an $r$-uniform hypergraph, which is defined as the sum of the absolute value of all the eigenvalues of its matching polynomial. With the aid of the matching polynomial of an $r$-uniform supertree, three pairs of $r$-uniform supertrees with the same spectral radius and the same matching energy are constructed, and two infinite families of $r$-uniform supertrees with the same spectral radius and the same matching energy are characterized. Some known results about the graphs with the same spectra regarding to their adjacency matrices can be naturally deduced from our new results.