Rice-duck farming is an organic farming system for the maintenance of soil fertility with duck manure. Such system helps reduce the pollutants induced by chemical fertilizers and pesticides use. Nevertheless, the productivity of such organic farming system is frequently limited due to the lack of sufficient chemical fertilizers. In order to supply sufficient soil nutrients, this paper proposes two-batch-duck raising with rice farming, including the rotational pasturing with two-batch-duck raising (RP) and the mixed pasturing with two-batch-duck raising (MP). The soil nutrients in these two proposed systems were monitored and compared with the ones in conventional rice monocropping (CR) and conventional rice-duck farming system (CD) through filed experiments. Compared with the CR treatment, the results showed that CD, RP and MP treatments led to the increase in the total N and total K contents. In addition, CD, RP and MP treatments resulted in less consumption of alkali-hydrolysis N. Soil organic matter (SOM) under these three treatments increased after harvesting, while it decreased in the CR treatment. All four treatments experienced significant reductions in the total soil P after harvest, of which less reductions were observed in the RP and MP treatments as compared to the CR treatment. Specifically, total soil P in the RP and MP treatments after early harvest was 13.53% and 11.01% higher than CR treatment, respectively. Compared with the CD treatment, both two-batch-duck raising systems led to the increased accumulation of SOM, total N and total P contents, and delayed the reductions in alkali-hydrolysis N, available P, available K, and total P in soil. Compared with the CD treatment, the contents of alkali-hydrolysis N, available P and available K in the MP treatment after harvest increased by 3.7%, 10.39% and 7.59%, respectively. Rice yield under MP treatment increased by 12.90% in the early rice season and 12.19% in the late season compared to CD treatment. These findings indicate that both the RP treatment and MP treatment outperform the CD treatment on soil fertility and nutrient utilization in paddy fields. This should be attributed to the increase in the pasture time in the two proposed systems with more duck feces and the effect of intertillage and muddying throughout the growing stages.