Based on the annual maximum peak flow data from the 6 hydrometry stations in the Beijiang River Basin, Top-kriging and ordinary kriging for regional flood frequency methods were respectively used to estimate area flood frequency. Root mean square error was used as a goodness of fit index of frequency distribution. Linear moment as a single station flood frequency analysis method was used to determine the design flood values of 10-year, 50-year, 100 year, 1000-year. Based on the above-mentioned, Top-kriging and ordinary kriging were compared in two aspects: design flood estimation uncertainty and single station flood frequency estimation error which based on linear moment method. The results show that: (1) Top-kriging is a better linear unbiased estimation, comparing to ordinary kriging method it is more suitable for area flood frequency estimation; (2) Top-kriging method of design flood estimation uncertainty is significantly less than the ordinary kriging; (3) Top-kriging method of design flood estimation is closer to the linear moment method single station flood frequency analysis.