Abstract: This study aims to elucidate the evolution of the storm-flood relationship in the Yinzhou Plain area of the Yongjiang Basin amidst changing environmental conditions. The responses of extreme water levels to heavy rains were analyzed over the period 1962 to 2021 at Jiangshan Station, considering disturbance characteristics and time-varying responses. The quantile disturbance method (QPM) and a time-varying correlation model were employed for this investigation. The findings revealed a significant increase in annual maximum 1-day/3-day precipitation and maximum water level, with rates of 8.39 mm/10a, 12.66 mm/10a, and 0.67 m/10a, respectively. The three indicators exhibited similar temporal perturbation patterns over the last 60 years according to QPM. Disturbances were predominantly negative from 1960 to 1984 and significantly positive from 2013 to 2021. Among the 12 selected models, the three time-varying models—Time-varying Normal, Time-varying Rotated Gumbel, and Time-varying Symmetrized Joe-Clayton—provided better fits for rainstorm-flood correlations. Generally, the response of annual maximum water level to annual maximum 3-day precipitation exhibited a stage characteristic of first rising and then falling. The high values of correlation were predominantly observed from the 1990s to the 2000s. These results enhance our understanding of the influence of urbanization on extreme precipitation-water level relationships and play a crucial role in the early warning and prediction of regional flood disasters.