The functionality and reliability of nanoscale multilayer devices and components are influenced by changes in stress and microstructure throughout fabrication, processing, and operation. NiV/B4C multilayers with a d-spacing of 3 nm were prepared by magnetron sputtering, and two groups of annealing experiments were performed. The stress, microstructure, and interface changes in NiV/B4C after annealing were investigated by grazing-incidence X-ray reflectometry (GIXR), grazing-incidence X-ray diffraction (GIXRD), X-ray diffuse scattering, and grazing-incidence small-angle X-ray scattering (GISAXS). The temperature dependence experiments revealed a gradual shift in the multilayer stress from compression to tension during annealing from 70 °C to 340 °C, with the stress approaching near-zero levels between 70 °C and 140 °C. The time-dependent experiments indicated that most of the stress changes occurred within the initial 10 min, which showed that prolonged annealing was unnecessary. Combining the X-ray diffraction and X-ray scattering measurements, it was found that the changes in the thickness, interface roughness, and lateral correlation length, primarily due to crystallization, drove the changes in stress and microstructure.