The effects of hyper-resistivity induced by anomalous electron viscosity on edge localized modes (ELMs) are systematically investigated using the ELM-PB model in BOUT++ simulation code. Our previous theoretical work [S Y Chen et al, Plasma Phys. Control. Fusion, 2024, 045001] indicates that the current diffusion caused by hyper-resistivity can reduce the magnetic field line bending stabilization effect and enhance the instability of ballooning modes. Meanwhile, the three-dimensional magnetohydrodynamic (MHD) simulations of peeling–ballooning mode (P–B mode) in this paper also indicate that hyper-resistivity can drive the instability of P–B mode. More specifically, when the value of normalized hyper-resistivity is large, the destabilizing effect is basically not affected by resistivity. Nonlinear simulations demonstrate that there exists a threshold value of normalized resistivity, below which, the loss of pedestal stored energy is mainly determined by hyper-resistivity. The three-dimensional MHD simulation result is consistent with our theoretical prediction that the influence of hyper-resistivity and resistivity on the P–B mode exhibits a competitive relationship. This implies that in future large-scale fusion devices with low-collisionality plasmas, the impact of hyper-resistivity on P–B mode instability will become non-negligible and may replace resistivity as a potential excitation mechanism for small ELMs.