AbstractTo study the dynamics in crop-field soil biodiversity under long-term fertilization is important for agricultural ecosystem protection. We selected a long-term fertilized paddy field under rice/rape rotation from the Taihu Lake region as a study site, and identified weed seeds in the topsoil (0–15 cm) by microscopic examination. Weed seed number and crop yields were recorded. We analyzed the effect of long-term fertilization on soil weed seed bank diversity and the relationship between weed seed diversity and crop yields. The fertilizer treatments were as follows: non-fertilizer (NF), chemical fertilizer only (CF), chemical fertilizer and pig manure combined (CMF), and chemical fertilizer plus crop stalk (CSF). The results indicated that in the cultivating seasons of both rice and rape, under the treatment of chemical fertilizer plus rice crop stalk, the density of soil weed seed bank was the lowest, whereas the total species number and diversity was the high-est. Furthermore, the crop yields were maximal and the steadiest under this treatment. There was definite correlation among fertilizer treatments, soil weed seed bank diversity and crop yields. It was concluded that balanced fertilizer management helps to maintain soil weed seed bank diversity, increase crop yields, and prevent crop yields from fluctuating. Therefore, among the four fertilizer treatments, chemical fertilizer plus rice crop stalk was the best one to increase the productivity of agricultural ecosystems and simultaneously protect biodiversity.