Abstract: Understanding the relationship between hydrological and sediment connectivity under extreme rainfall conditions is of great significance for water and sediment regulation and high-quality development of soil and water conservation in the basin under the new situation of vegetation restoration in the Loess Plateau. In this study, the influence of extreme rainfall and vegetation restoration on water-sediment connectivity and the characterization ability of sediment transport potential was analyzed based on the index of connectivity, the structural sediment connectivity (SC_st) improved by topographic location index and vegetation cover factor, the functional hydrological connectivity (HC_fn) improved by the cumulative surface runoff depth factor. The results showed that the rainfall and vegetation were the main functional and structural factors affecting hydrological and sediment connectivity, respectively. The mean value of normalized difference vegetation index (NDVI) increased by 0.41 from 2000 to 2020, while the mean value of sediment connectivity decreased by 3.54, with a negative correlation coefficient of −0.93. The spatio-temporal distribution of rainfall was in good agreement with the spatio-temporal distribution of hydrological connectivity, both of which were highly correlated on the monthly scale. When extreme rainfall occurred, rainfall runoff factors played a dominant role and determine hydrological and sediment connectivity. The improved water-sediment connectivity index was well applied to the study of large-scale watershed connectivity in the Loess Plateau. Pearson correlation analysis showed that the functional hydrolodical connectivity had a good correlation with runoff and sediment transport capacity in the basin under the inter-annual and seasonal variation, and could better reflect the phenomenon of runoff and sediment increase in the basin under extreme rainfall. Compared with previous studies in which functional connectivity was calculated by using factors such as rainfall erosivity under annual changes, which could not well characterize the actual sediment transport capacity of the basin, the functional connectivity used in this study had obvious advantages, which would provide a more direct and effective tool for water and sediment management in large basins on the Loess Plateau in the future. The interaction between basin structure and functional connectivity changed significantly with seasons. In dry season, vegetation cover was low, rainfall was low, structural sediment connectivity was high and HC_fn was increasing. At this time, SC_st had a weak influence on HC_fn, and the two showed a high negative correlation. In the wet season, with sufficient rainfall and lush vegetation, the correlation between structure and work connectivity changed with the trend of rainfall. At this time, the SCst was low, which limited the function of HC_fn to a certain extent. When encountering extreme rainfall, high-intensity rainfall runoff played a dominant role, and SCst couldn’t significantly affect HC_fn, while HC_fn changed SCst in turn, and both increased at the same time, showing a strong positive correlation. In the normal water season, vegetation gradually withered due to the weakening of rainfall intensity, SC_st increased while HC_fn decreased, and the negative correlation between the two was enhanced. In conclusion, the improved water-sediment connectivity index has certain advantages and limitations, which can provide guidance for water and sediment management and ecological construction of large watershed in the Loess Plateau under the changing environment in the new era.