Hydrological connectivity is an important stability indicator of the pattern and function of wetlands. A decrease in hydrological connectivity of wetlands usually indicates the degradation of ecological functions, and the disruption of internal energy flow and nutrient circulation. Baiyangdian Lake is the most typical and representative wetland in Beijing, Tianjin, and Hebei provinces. Based on morphological spatial pattern analysis (MSPA) and connectivity indices, we chose Baiyangdian Lake as a study case for analyzing the changes in its hydrological connectivity at the spatial and temporal scales, and for summarizing the morphological and spatial processes. The results show that the hydrological connectivity of the Baiyangdian wetland was generally weak from 1990 to 2015, which reduced between 1990 and 2005, but gradually recovered thereafter. The mechanism of spatial and temporal evolution of the Baiyangdian wetland can be divided into two stages according to the changes in landscape function type of the MSPA: the period of degradation between 1990 and 2005, and the period of recovery between 2005 and 2015. During the period of degradation, the core wetlands were partly divided into fine patches such as branches, loops, bridges, and islets, and then disappeared gradually. During the recovery period, the core wetlands extended, whereas the branches converted to bridges. The core wetland area decreased from 9974.90 hm² in 1990 to 2209.97 hm² in 2005 and increased thereafter to 4122.14 hm² in 2015. The changes in area and morphology of core wetlands dominated the changes in hydrological connectivity of the Baiyangdian wetland. The driving factors for the decrease of hydrological connectivity in Baiyangdian wetland are mainly the amount of upstream recharge water, land use changes, and climate change. The present study shows that the MSPA model combined with connectivity indices can explain the organization and operation mechanism of wetland hydrological connectivity well, which would provide essential background for other related studies.