Using the water footprint theory, the different types of water footprints of 13 cities in Heilongjiang Province from 2000 to 2018 were quantified, and their spatio-temporal distribution was analyzed. The differences of water footprints in various regions were studied by combining the spatial balance analysis. The results showed that the total water footprint of Heilongjiang Province showed a rising trend from 2000 to 2018, of which the grey water footprint had been decreasing. In 2018, the per capita grey water footprint was 300.7.m³. The spatial distribution of water footprint is uneven, and the abundant water footprint and the lack of water footprint coexist. On the whole, it shows a trend of low in the north, high in the south, low in the east and high in the west. During the study period, the spatial distribution of the per capita grey water footprint and the per capita water footprint in Heilongjiang Province is relatively uniform, and the overall spatial equilibrium degree is higher than 0.6. The spatial distribution of water footprint intensity, industrial blue water footprint and ecological blue water footprint are quite different. The overall spatial equilibrium degree of water footprint is gradually rising, but the maximum value is not more than 0.6, and there are still large differences in regional distribution.