In this paper, we would like to systematically explore the implications of non-perturbative effects on entanglement in a many body system. Instead of pursuing the usual path-integral method in a singular space, we attempt to study the wavefunctions in detail. We begin with a toy model of multiple particles whose interaction potential admits multiple minima. We study the entanglement of the true ground state after taking the tunnelling effects into account and find some simple patterns. Notably, in the case of multiple particle interactions, entanglement entropy generically decreases with increasing number of minima. The knowledge of the subsystem actually increases with the number of minima. The reduced density matrix can also be seen to have close connections with graph spectra. In a more careful study of the two-well tunnelling system, we also extract the exponentially suppressed tail contribution, the analogues of instantons. To understand the effects of multiple minima in a field theory, it inspires us to inspect wavefunctions in a toy model of bosonic field describing quasi-particles of two different condensates related by Bogoliubov transformations. We find that the area law is naturally preserved. This is probably a useful set of perspectives that promise wider applications.