Using daily station data and Japanese 55-year Reanalysis Project (JRA-55) data from 1959 to 2013, a three-dimensional background circulation structure of summer heavy rainfall in the middle–lower reaches of the Yangtze River (MLYR) was analyzed. Composite analyses of circulation in advance of 373 heavy rainfall days revealed that a prominent warm anomaly with a center at 300 hPa emerged in the upper troposphere over the MLYR. Because of hydrostatic and quasi-geostrophic equilibriums, an anticyclonic (cyclonic) anomaly formed above (below) the warm center. On the one hand, the warm anomaly strengthened the westerly winds to the north of the warm center by a high-level anticyclonic circulation anomaly, which resulted in the jet stream in the upper-level over East Asia shifting southward and eastward to the north side of the MLYR. This enhanced the upper-level divergent anomaly field over the MLYR. On the other hand, the cyclonic anomaly below the warm anomaly reinforced the low-level southwesterly winds to the MLYR, which transported more water vapor to it and strengthened convergence. The favorable configuration of high and low altitude circulation anomalies caused by warm anomalies played an important role in the formation of strong precipitation in the MLYR. The 300 hPa warm anomaly existed at 400–300 hPa in the eastern part of the Qinghai-Tibet Plateau 48 hours before the precipitation in the MLYR. The 700 hPa cyclonic circulation appeared in the middle and lower layers over the Sichuan Basin 24 hours ahead of schedule. The high and low circulation elements cooperated with each other and moved eastward with time. The warm anomaly first reached the MLYR, and cooperated with the low-level cyclonic circulation and water vapor convergence area, resulting in strong precipitation over the MLYR.