Heilongjiang Province is one of the most important commodity grain bases in China. Because the territory of Heilongjiang Province is very vast, and the natural conditions and management mode are different, the diversity of irrigation water use efficiency in different regions in Heilongjiang Province is very remarkable. In 2013, the average irrigation water use efficiency in Heilongjiang Province was only 53%, which was lower than the average level in China. Therefore, in order to study the problems of low irrigation water use efficiency in Heilongjiang Province, the spatial distribution and influencing factors of irrigation water use efficiency index system were analyzed according to the geo-statistics theory by using GIS technology. The results showed that for the variation coefficients of all the variables, the intact rate of irrigation engineering was the biggest, and the evapotranspiration was the smallest. The field water use efficiency had the greatest influence; its positive spatial autocorrelation range was 145 km. And the positive spatial autocorrelation range of irrigation water use efficiency was 124 km; the water conveyance efficiency was mainly affected by random factors, its scale of positive spatial autocorrelation was 73 km. The Kriging maps showed that the three indexes had high values in Daqing, Harbin, Suihua Cities and their vicinities. The influence of natural factors was less than that of human factors on irrigation water use efficiency. There were negative correlations respectively between rainfall and irrigation water use efficiency, field water use efficiency. Improving the proportion of irrigation water saving area and the intact rate of irrigation engineering had significant driving to field water use efficiency and the water conveyance efficiency. The study results had important significance to the improvement of water saving in different regions in Heilongjiang Province.