We investigate the magnetic response in the quantized spin Hall (SH) phase of layered-honeycomb lattice system with intrinsic spin-orbit coupling lambda_SO and on-site Hubbard U. The response is characterized by a parameter g= 4 U a^2 d / 3, where a and d are the lattice constant and interlayer distance, respectively. When g< (sigma_{xy}^{s2} mu)^{-1}, where sigma_{xy}^{s} is the quantized spin Hall conductivity and mu is the magnetic permeability, the magnetic field inside the sample oscillates spatially. The oscillation vanishes in the non-interacting limit U -> 0. When g > (sigma_{xy}^{s2} mu)^{-1}, the system shows perfect diamagnetism, i.e., the Meissner effect occurs. We find that superlattice structure with large lattice constant is favorable to see these phenomena. We also point out that, as a result of Zeeman coupling, the topologically-protected helical edge states shows weak diamagnetism which is independent of the parameter g.