In three-dimensional configurations, the confinement region is surrounded by the stochastic magnetic field lines related to magnetic islands or separatrix, leading to the fact that the plasma–vacuum boundary is not so definite compared with tokamaks that the various modulations of the plasma–vacuum boundary will be induced around the stochastic region by synergetic effects between a transport around the stochastic region and a large Shafranov shift of the whole plasma, in especially high-β operations. To examine such modulation effects of the plasma boundary on MHDinstabilities, high-β plasmas allowing a large Shafranov shift or a large Pfirsch–Schl¨uter current are considered in the inward-shifted LHD configurations with the vacuum magnetic axis Rax of 3.6 m, for which previous theoretical analyses based on fixedMHDequilibria indicate that pressure-driven modes are significantly more unstable compared with experimental observations. The concept of the averaged flux surfaces allowing a movement of the equilibrium plasma into the stochastic region is introduced, which induces a boundary modulation and, at the same time, reduces the discrepancy on MHD equilibria between the experimentally obtained and theoretically considered. As a result, it is shown that the boundary modulation, namely, the whole plasma outward-shift due to a large Pfirsch–Schl¨uter current has significant stabilizing effects on ideal MHD instabilities, leading to partially resolving the discrepancy on MHD stability between experimental results and theoretical analyses.