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Reduced tillage provides ecological and economic benefits to arable land on the Loess Plateau of China, where soil erosion has long been a serious problem and soil water availability is largely restricted. However, high abundances of weeds in reduced tillage systems cause significant yield losses. In this study, we explored the effects of no-tillage and stubble retention on the number and density of weeds and weed seeds in a 12-year maize-winter wheat-common vetch rotation on the Loess Plateau. Four treatments including conventional tillage, no-tillage, conventional tillage+stubble retention and no-tillage+stubble retention were designed and applied. We found that no-tillage increased the number of weed species and weed density in most of the crops, while stubble retention decreased weed density in maize and tended to suppress weeds in both no-tillage treatments (no-tillage and no-tillage+stubble retention). No-tillage led to an increase in the number of weed species in the weed seedbank and tended to increase seed density during the spring growth of winter wheat, but it decreased seed density during post-vetch fallow. Stubble retention tended to reduce seed density during the spring growth of winter wheat and post-vetch fallow. We concluded that no-tillage can promote weeds in the experimental crop rotation, while stubble retention suppresses weeds in untilled fields. The combined effects of stubble retention and no-tillage on weed suppression varied among the three crops. Based on these results, we recommend stubble retention in untilled legume-crop rotations on the Loess Plateau to improve the control of weeds.