In order to investigate the fractal characteristics and influence factors of irrigation water use efficiency in different scales irrigation areas, the measuring results of irrigation water use efficiency in 115 different scales irrigation area were selected as samples during 2009—2014. The fractal characteristics of above samples were studied by using the method of rank-size distribution, and the influence factors of irrigation water use efficiency of Heilongjiang province were analyzed by using principal component analysis. The result showed that the fractal dimension value D of irrigation water use efficiency of Heilongjiang province was ranged in 5.26~6.25 in 2009—2014, and the distribution of irrigation water use efficiency changed from multifractal structure to single fractal structure. For the largemiddle scale irrigation area (D1=4.58), irrigation water use efficiency was the maximum of 44.44%. For the miniature irrigation area (D2=4.79), irrigation water use efficiency was the maximum of 53.81%. For the pure well irrigation area (D3=6.98), irrigation water use efficiency can reach maximum of 70.41%. For the whole province (D=5.13), irrigation water use efficiency can reach maximum value of 57.03%. In the influence factors analysis for irrigation water use efficiency of different scales irrigation area, the channel lining rate and engineering equipment rate were the most two influential factors to irrigation water use efficiency of largemiddle scale irrigation area. To miniature irrigation area, the influence of the channel lining rate was the most, and the influence of the ratio of evaporation to transpiration was the least. Field leakage was the most influential factor to irrigation water use efficiency of pure well irrigation area. The research results provided a theoretical basis for the balanced promotion of irrigation water use efficiency in Heilongjiang province.