Three cotton fields located on the northern slope of Tianshan Mountains, along the gradient from the oasis to the edges of desert, were selected as our experimental sites. We analyzed the effects of flood irrigation and drip irrigation on the spatiotemporal variation of soil seed banks for the first 4 years and the 8th year. The results showed that drip irrigation had a larger effect on the seed banks of weeds in cotton fields, as the species number and seed density per unit area fluctuated significantly between the years. Continuous drip irrigations changed the structure and the composition of soil seed banks; number of species decreased from 27 species by flood irrigations to 20 and 15 species after 1 and 8 years of drip irrigation respectively. The Shannon-Wiener diversity index reached the lowest for the 8th year drip irrigation and seed density per unit area dropped substantially. With the increase of drip irrigation duration, the species-Chloris virgata, Lotus corniculatus, Descurainia sophia, Polygonum lapathifolium, Atriplex centralasiatica and Dodartia orientalis etc, were found to be affected considerably, while species, such as Setaria viridis, Chenopodium album, Chenopodium glaucum, Solanum nigrum, Portlulaca oleracea, Amaranthus lividus, Cirsium setosuum, Artemisia annua, Sonchus oleraceus, Conyza canadensis, Capsella bursapastoris, C. serotinum, Polygonum aviculare, Abutilon theophrasti, Convolvulus arvensis and Mentha haplocalyx adapted well owing to their wide time niche breadth and spatial niche breadth, especially the Setaria viridis, Chenopodium album, Solanum nigrum, A.retroflexus and Amaranthus lividus, which were found in dryer conditions. The ratio of these species in all seed banks increased gradually and they were the dominant weeds in the cotton fields. Affected by tillage methods, the seed banks of weeds were mainly distributed in the farming layer. The seed number was the lowest beyond the farming layer from 46cm to 50cm. Analysis of horizontal distribution patterns revealed that species at the three sites were very similar. The irrigation methods, flood irrigation and drip irrigation, appeared to have greater impact on the species variation than the difference of geographical locations.