This study compared the impacts of different weed managements on weed community, soil health and economic performance between the wheat–maize (WM) and garlic–soybean (GS) rotations. A total of four treatments (H0T, tillage without herbicide; H0T0, without both herbicide and tillage; HT, both herbicide and tillage; HT0, herbicide without tillage) were designed for both rotations. A total of 16 weed species were recorded in the WM rotation, with life forms of 62% for annuals, 12% for annual + perennial and 20% for perennials. While in the GS rotation, there were 17 weed species, with 71% being annuals. When crop rotation changed from WM to GS, the topsoil layer seed bank (0–5 cm) decreased by 137%. GS rotation always had higher earthworm densities than that of WM under the same condition. Organic weed control (H0T, H0T0) from both WM and GS added more soil organic matters than the chemical methods (HT and HT0). Economically, up to 69% higher net profit had been achieved in the GS than WM for their organic products. This study provides an ecological basis to guide organic farming practices, especially for weed management in the future.