Compared with NPK treatment, the application of NPK + organic manure increased the abundance of all the nitrogen-cycling genes while the application of NPK + wheat straw had little effect. The abundance of amoA genes contributed the most to the variations in the abundance of the nitrogen cycling community between different fertilization strategies. Soil available P and total N were the most important factors influencing the abundance of microbial communities involved in the nitrogen cycle. These results indicated that, under the application of chemical fertilizers, the addition of livestock manures had much stronger effects on the abundance of nitrogen cycle genes than the addition of wheat straw, and bacterial and archaeal amoA genes were more sensitive to fertilization than other functional genes.