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The Yangtze–Huai River Basin (YHRB) always suffers from anomalously heavy rainfall during the warm season, and has been well explored as a whole area during the past several decades. In this study, the YHRB is divided into two core regions — the northern YHRB (nYHRB) and southern YHRB (sYHRB) — based on 29-year (1979–2007) June–July–August (JJA) temporally averaged daily rainfall rates and the standard deviation of rainfall. A spectral analysis of JJA daily rainfall data over these 29 years reveals that a 3–7-day synoptic-timescale high-frequency mode is absolutely dominant over the nYHRB, with 10–20-day and 15–40-day modes playing a secondary role. By contrast, 3–7-day and 10–20-day modes are both significant over the sYHRB, with 7–14-day, 15–40-day, and 20–60-day modes playing secondary roles. Based on a comparison between bandpass-filtered rainfall anomalies and original rainfall series, a total of 42, 1, 5, and 3 heavy rainfall events (daily rainfall amounts in the top 5% of rainy days) are detected over the nYHRB, corresponding to 3–7-day, 7–14-day, 10–20-day, and 15–40-day variation disturbances. Meanwhile, a total of 28, 8, 12, and 6 heavy rainfall events are detected over the sYHRB, corresponding to 3–7-day, 7–14-day, 10–20-day, and 20–60-day variation disturbances. The results have important implications for understanding the duration of summer heavy rainfall events over both regions.