At the nanoscale, elastic strain and crystal defects largely influence the properties and functionalities of materials. The ability to predict the structural evolution of catalytic nanocrystals during the reaction is of primary importance for catalyst design. However, to date, imaging and characterising the structure of defects inside a nanocrystal in three-dimensions and in situ during reaction has remained a challenge. We report here an unusual twin boundary migration process in a single platinum nanoparticle during CO oxidation using Bragg coherent diffraction imaging as the characterisation tool. Density functional theory calculations show that twin migration can be correlated with the relative change in the interfacial energies of the free surfaces exposed to CO. The x-ray technique also reveals particle reshaping during the reaction. In situ and non-invasive structural characterisation of defects during reaction opens new avenues for understanding defect behaviour in confined crystals and paves the way for strain and defect engineering.