The weakened connectivity of wetland systems is the key factor leading to the destruction, degradation, and disappearance of wetlands. The study of the change of wetland system connectivity enables understanding the hydrological process in wetland system and providing significant support for the study of ecological water demand. However, research on the connectivity of wetland systems has primarily focused on the intuitive connectivity in terms of hydrology and geomorphology in recent years, while the impact of wetland systems on habitat has been ignored. In this study, an innovative method was applied to evaluate and regulate the stereoscopic spatial connectivity (SSC) of the wetland system in the Heilongjiang River Basin in China (HRBC). In this method, the water requirements of typical organisms in the region were considered, and the hydrological trend in the wetland system as well as the health conditions of the SSC were analyzed using remote sensing image. A regulation mode for improving the stereoscopic spatial connectivity index (SSCI) was proposed. The results revealed that over the past 35 years, the wetland system in the study area shrank significantly, with the SSCI decreasing from 41.30% in 1980 to 35.08% in 2015. By comparing the correlation among temperature, precipitation, agricultural land, construction land, and the wetland system during the same period, it was proven that human activity is the major driving force behind the observed wetland system shrinkage. Subsequently, the key protected areas required to maintain the SSC of the wetland system were clarified, and the key recovery areas were determined according to the three scenarios of ‘high–medium–low’ feasibility, which greatly improved the SSCI and generalization route (GR) after regulation. In general, the proposed SSC evaluation methods can fully reflect the ecohydrological process of wetland systems. The methods also scientifically quantify the significant effects of the regulation mode, which has certain relevance for the evaluation and regulation of wetland systems in other regions.