Based on the daily rainfall data of 79 rainfall stations in the upper reaches of the Yangtze River Basin from 1979 to 2019 and the daily runoff data at the Three Gorges, the concurrent relationship between the rainy season onset and the runoff-based flood season onset in the upper reaches of the Yangtze River Basin under different threshold discrimination conditions was explored. Based on the correlation coefficients between the rainy season onset dates and the runoff-based flood season onset dates under different thresholds, the respective thresholds for rainfall and runoff when their relationship was the most significant were determined, and accordingly, the rainy season onset index and the runoff-based flood season onset index of the upper reaches of the Yangtze River Basin were determined. The results indicate that the increase in rainfall in the upper reaches of the Yangtze River Basin precedes the rise of the inflow at the Three Gorges by 2-4 pentads. Before the flood season onset, the most significant increase in rainfall occurs at the 30th pentad, and the corresponding inflow at the Three Gorges shows an obvious rise at the 32nd pentad; the multi-year average dates of the rainy season onset and the runoff-based flood season onset are May 31 and June 11, respectively. In most years from 1979 to 2019, the rainy season onset date is earlier than the runoff-based flood season onset date, but there are eight years when the rainy season onset is slightly later than the runoff-based flood season onset, mainly because the number of rainfall stations meeting the standard in the rainy season onset index is insufficient. After optimizing the rainy season onset index using the basin rainfall volume index, the optimization effect is remarkable, and there are only two years when the rainy season onset date is later than the runoff-based flood season onset date.