The conservation management of biodiversity hotspots is of vital significance for biological conservation. For wetlands, which are a special type of ecosystems that are based on water as their main medium, a decline in external hydrological connectivity often leads to wetland degradation inside biodiversity hotspots. In this context, the relationship between hydrological connectivity changes inside and outside hotspots is worth exploring. Based on the wetland biodiversity hotspots identified using systematic conservation planning, this study selected eight representative biodiversity hotspots with concentrated area. Integral index of connectivity, probability of connectivity (representing structural connectivity), and morphological spatial pattern analysis (representing functional connectivity) were used to analyze the hydrological connectivity changes inside various hotspots for 1995–2015. By taking the catchment area involved as the minimum basin perimeter, this study calculated the external hydrological connectivity changes of various hotspots during this period and analyzed the relationship between hydrological connectivity changes inside and outside of hotspots. The internal and external hydrological connectivity of wetland biodiversity hotspots were found to be significantly correlated. Moreover, the internal hydrological connectivity of hotspots not only declined with declining external structural connectivity, but also changed with the proportion of core wetlands, the proportion of edge wetlands, and the proportion of branch corridors. In addition, hotspots located at intersections of high-grade rivers were more significantly affected by climate change than by human activities and their hydrological connectivity increased with increasing rainfall. The internal hydrological connectivity of hotspots near low-grade rivers presented a declining trend, mainly because of human activities. This study clarified the relationship between internal and external hydrological connectivity of wetland biodiversity hotspots. Targeted internal and external control strategies are proposed, with the aim to offer references for the conservation of wetland biodiversity.