The article deals with the effects of urea and controlled release nitrogen fertilizer (CRNF) on dynamics of pH, electronic conductivity (EC), total nitrogen (TN), NH4+-N and NO3--N in floodwater, and the regulation of runoff TN loss from paddy field-based two-cropping rice in Dongting Lake, China, and probes the best fertilization management for controlling N loss. Studies were conducted through modeling alluvial sandy loamy paddy soil (ASP) and purple calcareous clayey paddy soil (PCP) using lysimeter, following the sequence of the soil profiles identified by investigating soil profile. After application of urea in paddy field-based two-cropping rice, TN and NH4+-N concentrations in floodwater reached peak on the 1st and the 3rd day, respectively, and then decreased rapidly over time; all the floodwater NO3--N concentrations were very low; the pH of floodwater gradually rose in case of early rice within 15 d (late rice within 3 d) after application of urea,and EC remained consistent with the dynamics of NH4+-N. The applied CRNF, especially 70% CRNF, led to significantly lower floodwater TN and NH4+ concentrations, pH, and EC values compared with urea within 15 d after application. The monitoring result for N loss due to natural rainfall runoff indicated that the amount of TN lost in runoff from paddy fieldbased two-cropping rice with urea application in Dongting Lake area was 7.47 kg ha-1, which accounted for 2.49% of ureaN applied, and that with CRNF and 70% CRNF application decreased 24.5 and 27.2% compared with urea application,respectively. The two runoff events, which occurred within 20 d after application, contributed significantly to TN loss from paddy field. TN loss due to the two runoffs in urea, CRNF, and 70% CRNF treatments accounted for 72, 70, and 58% of the total TN loss due to runoff over the whole rice growth season, respectively. And the TN loss in these two CRNF treatments due to the first run-off event at the 10th day after application to early rice decreased 44.9 and 44.2% compared with urea, respectively. In conclusion, the 15-d period after application of urea was the critical time during which N loss occurred due to high floodwater N concentrations. But CRNF decreased N concentrations greatly in floodwater and runoff water during this period. As a result, it obviously reduced TN loss in runoff over the whole rice growth season.