The change of drought and flood in southwestern China is affected by many weather systems. The intensity change of the Qinghai-Tibetan Plateau summer monsoon (QTPSM) and boreal summer intraseasonal oscillation (BSISO) sub-seasonal system will lead to change of drought and flood in rainy season of southwestern China, but the systematic research on synergy of the two systems on precipitation was scarce at present. Therefore, based on the daily precipitation data from Climate Prediction Center of National Oceanic and Atmospheric Administration and daily reanalysis data from National Centers for Environmental Prediction during 1981-2020, etc., we analyze the individual and joint influence mechanism of QTPSM and BSISO on drought and flood in rainy season of southwestern China by using the Qinghai-Tibetan Plateau monsoon index (QTPMI) and BSISO index. The results are as follows: (1) The intensity of QTPSM is negatively correlated with precipitation in rainy season of southwestern China, and the active QTPSM (AQ) inhibits precipitation, while the inactive QTPSM (IAQ) promotes precipitation. (2) The probability of extreme precipitation in rainy season of southwestern China increases at 5 and 6 phase of the first mode and 3 and 4 phase of the second mode of BSISO, while that of extreme precipitation decreases at 2 and 3 phase of the first mode and 6 and 7 phase of the second mode of BSISO. (3) At the combined stage of 6 and 7 phase of the second mode of BSISO with QTPSM, their joint influence on drought and flood in rainy season of southwestern China is the greatest, and the positive anomalous distribution of precipitation is the widest. When BSISO phase combining with AQ changes to IAQ, the large value area of positive precipitation anomaly shifts from north to south of southwestern China. (4) At the combined phases of AQ in rainy season, the southeast winds prevail in the middle troposphere over southwestern China, and the circulation configuration in lower troposphere with “one high and one low” controls on the east and west sides of southwestern China, which urges water vapor from the Indian Ocean and the western Pacific to transport the north of southwestern China, and forms water vapor convergence area. By contrast, at the combined phases of IAQ, the northerly winds prevail in middle troposphere over southwestern China, and the strong cyclone controls in lower layer, which leads water vapor from the Indian Ocean to transport persistently into the south of southwestern China, and forms the water vapor convergence zone.