This article discusses the misalignment, surface deviations, and thermal deformation of the submillimetre wave instrument (SWI) optics on the Jupiter Icy Moons Explorer (JUICE) mission and how they are included into the optical model of the instrument. Misalignment and surface deviations caused by the manufacturing and assembly were measured with a coordinate measurement machine. Finite element method simulations determined thermoelastic deformation of the optics from room temperature to operational temperatures between -70 °C and -130 °C. The optical performance of the instrument was simulated for several telescope pointing angles using the optical model for these imperfections.