The determination of the pairing symmetry is one of the most crucial issues for the iron-based superconductors, for which various scenarios are discussed controversially. Non-magnetic impurity substitution is one of the most promising approaches to address the issue, because the pair-breaking mechanism from the non-magnetic impurities should be different for various models. Previous substitution experiments demonstrated that the non-magnetic zinc can suppress the superconductivity of various iron-based superconductors. Here we demonstrate the local destruction of superconductivity by non-magnetic zinc impurities in Ba0.5K0.5Fe2As2 by exploring phase-slip phenomena in a mesoscopic structure with 119 × 102 nm 2 cross-section. The impurities suppress superconductivity in a three-dimensional 'Swiss cheese'-like pattern with in-plane and out-of-plane characteristic lengths slightly below ∼1.34 nm. This causes the superconducting order parameter to vary along abundant narrow channels with effective cross-section of a few square nanometres. The local destruction of superconductivity can be related to Cooper pair breaking by non-magnetic impurities.