In this article, we study the space of subgroups of non-amenable generalized Baumslag-Solitar groups (GBS groups) of rank d, that is, groups acting cocompactly on an oriented tree with vertex and edge stabilizers isomorphic to $\mathbb {Z}^d$
. Our results generalize the study of Baumslag-Solitar groups, and of GBS groups of rank $1$
. We give an explicit description of the perfect kernel of a non-amenable GBS group G of rank d and show the existence of a partition of the perfect kernel into a countably infinite set of pieces that are invariant under the action by conjugation of G, and such that each piece contains a dense orbit.