The source area of the Yellow River (SAYR) in China is an important water yield and water-conservation area in the Yellow River. Understanding the variability in rainfall and flood over the SAYR region and the related mechanism of flood-causing rainfall is of great importance for the utilization of flood water resources through the optimal operation of cascade reservoirs over the upper Yellow River such as Longyangxia and Liujiaxia, and even for the prevention of flood and drought disasters for the entire Yellow River. Based on the flow data of Tangnaihai hydrological station, the rainfall data of the SAYR region and NCEP-NCAR reanalysis data from 1961 to 2020, three meteorological conceptual models of flood-causing rainfall—namely westerly trough type, low vortex shear type, and subtropical high southwest flow type—are established by using the weather-type method. The mechanism of flood-causing rainfall and the corresponding flood characteristics of each weather type were investigated. The results show that during the process of flood-causing rainfall, in the westerly trough type, the mid- and high-latitude circulation is flat and fluctuating. In the low vortex shear type, the high pressures over the Ural Mountains and the Okhotsk Sea are stronger compared to other types in the same period, and a low vortex shear line is formed in the west of the SAYR region at the low level. The rain is formed during the eastward movement of the shear line. In the subtropical high southwest flow type, the low trough of Lake Balkhash and the subtropical high are stronger compared to other types in the same period. Flood-causing rainfall generally occurs in areas with low-level convergence, high-level negative vorticity, low-level positive vorticity, convergence of water vapor flux, a certain amount of atmospheric precipitable water, and low-level cold advection. In terms of flood peak increment and the maximum accumulated flood volume, the westerly trough type has a long duration and small flood volume, and the low vortex shear type and the subtropical high southwest flow type have a short duration and large flood volume.