How to identify the spatial flow processes and matching characteristics of water supply services in natural-human social systems is important for regional water resources management and sustainable utilization. Taking Chongqing as the study area, the water supply and water demand at the watershed scale in Chongqing from 2000 to 2020 were quantitatively assessed based on the InVEST model and socio-economic development perspective. Combining the water security index and hotspot analysis to build a water supply service flow model, we reveal the spatial matching relationship between supply and demand of water supply services, and classify the regional types of supply and demand matching relationship based on the spatial attribute characteristics of water supply service flow. On this basis, the factors influencing the matching relationship between supply and demand of water supply services for each regional type are discussed from three perspectives: natural, social and ecological with the use of the Geodetector. The results show that (1) From 2000 to 2020, the supply and demand of water in the Chongqing watershed first decreased and then increased, and the average value of the supply-demand ratio was 1.17, 1.08, and 0.9, respectively. Overall supply-demand mismatch gradually easing, but localized mismatch still exists. The areas of medium to high spatial deficit are concentrated within the main urban area, radiating outwards into areas of mild deficit, and the surplus areas are distributed in the north-eastern and south-eastern directions. (2) From 2000 to 2020, the cold and hot spot range of water supply and demand ratios was shrunk in Chongqing, and the watershed area was relatively reduced by 25.34% and 9.2%, respectively. The water supply service flow spatially showed an overall flow path from the northeast and southeast to the west, while the cold spot area presented edge-to-center flow within the area. (3) The confluence area was concentrated in the northwest, the meridian area was located in the middle, and the outflow area was concentrated in the southeast and the northeast. The dominant factor affecting the supply-demand matching relationship in the confluence area is evapotranspiration, with an explanatory power of 74.08%; the dominant factor affecting the meridional area is the tertiary GDP, with an explanatory power of 51.44%; the explanatory power of all influencing factors in the outflow area is low. Interaction of evapotranspiration with other factors was significantly higher among different impact factors. The study can provide a scientific basis for the management of natural resources and the establishment of watershed ecological compensation mechanisms in Chongqing.