PbS quantum dot (QD) solar cells demonstrate great potential in solar energy conversion with a broad and flexible spectral response. Even though long-term storage stabilities of QD solar cells were reported in literature, the operation stability from a more practical aspect, to date, has been not yet investigated. Herein, we observe the structure degradation process of a PbS QD-ink based solar cell during the device operation. Simultaneously to probing the solar cell parameters, the overall structure evolutions of the QDs in both, active layer and hole transport layer of the solar cell are studied with grazing-incidence small- and wide-angle X-ray scattering (GISAXS/GIWAXS). We find a spontaneous decrease of the QD inter-dot distance with an increase in the spatial disorder in the active layer (PbX2-PbS QDs, X = I, and Br) during the operation induced degradation. Consequently, the structure disorder-induced broadening of the energy state distribution is responsible for the decrease in open-circuit voltageVocleading to the device degradation. These findings elucidate the origin of light-soaking as well as the structure degradation of QD ink-based solar cells and indicate that the stability of the device can be realized by the positional stabilization of the QDs in the QD solid.