In order to provide a scientific basis for simplified cultivation of rapeseed in the Yangtze River Basin, a long-term (2011—2016) field experiment was carried out in Jianghan Plain to study the effects of different fertilization models on rapes, weeds, soil nutrients, and the spatial distribution of winter rapes-weeds in a rotation system of rice-winter rape. Through field investigation and lab analysis, the data of weed communities and of nutrient status in rape-weed-soil system were obtained during the rape harvest season in 2016. The results showed that soil nutrient deficit significantly affected the growth and spatial distribution of both rapes and weeds, and could influence the formation of different weed communities. However, balanced fertilization obviously increased the thickness of rape roots, the numbers of branch and pod as well as the final yield, and also reduced weed biomass and increased Shannon index. Compared with NPK treatment, separate –N, –P and –K treatments reduced nutrient uptake of rape grain, stem and shell as well as weeds to different degrees, especially for –P treatment. Long-term fertilization deficits reduced soil N, P and K contents compared to the initial values, especially for K. The existing balanced fertilization measures were not sufficient to offset K deficiency, indicating the importance of returning straw K to field. Overall, long-term scientific nutrient management and regulation can not only reduce damage from weeds, strengthen biodiversity of rape, form a favorable competitive environment for rape, but also can reduce pesticide use and promote simplified cultivation of rape in South China.