The standard cosmological model assumes a homogeneous and isotropic universe as the background spacetime on large scales called the cosmological principle. However, some observations suggest the possibility of an inhomogeneous and anisotropic universe at large scales. In this paper, we investigate a model of the Universe with random inhomogeneities and anisotropies on very large scales, motivated by the supercurvature dark energy model in Nan et al. [Phys. Rev. D 99, 103512 (2019)]. In this model, the authors introduced a scalar field with $\mathcal{O}(1)$ inhomogeneities on a scale sufficiently larger than the current horizon scale (superhorizon scale), and the potential energy of the scalar field explains the accelerating expansion, with slight deviations from the cosmological principle. We aim at clarifying the theoretical prediction on the large-scale structure (LSS) of the matter component in this model. Based on the work on the superhorizon scale fluctuations (superhorizon mode) presented in Y. Nan and K. Yamamoto [Phys. Rev. D 105, 063518 (2022)], we derive the equations that the perturbative components to the LSS obey as a generalization of the cosmological perturbations theory, which is solved to find the influence of the dark energy inhomogeneities on the formation of the LSS. Finally, we show that the model can be consistent with observations by comparing the ${\ensuremath{\sigma}}_{8}$ predicted by the numerical solution of the model with the ${\ensuremath{\sigma}}_{8}$ indicated by observations such as Planck and the Sloan Digital Sky Survey.