Based on the NCEP/NCAR daily reanalysis data and the daily rainfall data of ground observation at 164 weather stations in the middle and lower reaches of the Yangtze River from 1960 to 2013, the relationship between South Asia high low frequency oscillation and the drought and flood in the middle and lower reaches of the Yangtze River were analyzed using a composite analysis, wavelet analysis and band-pass filtering analysis method. The results indicated that in the typical drought and flood years, the Qinghai-Tibet Plateau 200 hPa atmosphere u, v low-frequency primary cycle and the summer rainfall cycle over the middle and lower reaches of the Yangtze River were the same. In more summer rainfall, from the Qinghai-Tibet Plateau to east China and west Pacific coast, there existed a cycle-anticyclone-cycle low frequency wave train. Low-frequency anticyclone controlled eastern China and the low-frequency cyclone controlled the northern Qinghai-Tibet Plateau. In drought years, results were opposite. In flood years, the precipitation of low frequency over the middle and lower reaches of the Yangtze River and that of 200 hPa atmospheric low frequency change of the Qinghai-Tibet Plateau was closely related. When the northerly wind in the northeast part of the the Qinghai-Tibet Plateau and in the middle and lower reaches of the Yangtze River was strong, and Lake Baikal southerly wind was strong, there was more precipitation. On the contrary, precipitation was less. The low frequency oscillation wave train was mainly spread from the northeast of China and Japan's southern to China’s southwest. However, in drought years, the relationship between them was not clear and needed to be further studied.