Fertilization is an important technology for the improvement of agricultural production capacity in arid areas in northern China. It is of great significance to study the influence mechanism of soil microbial community structure and functional genes of nitrogen cycle on nitrogen utilization efficiency (NUE) on soil nutrient management and fertility improvement. This study was based on the long-term fertilization positioning test established in 1988 in the loess Plateau, conducted (1) single nitrogen fertilizer (N), (2) single organic fertilizer (M), (3) nitrogen fertilizer increased lower organic fertilizer (M1N), (4) nitrogen fertilizer increased higher organic fertilizer (M2N), (5) no fertilization (CK) as a control. High-throughput sequencing, metagenomic sequencing and bioinformatics analysis were used to clarify the structure of soil microbial community composition, diversity characteristics and change of major functional genes related to nitrogen cycle, explored the microbial driving mechanism of nitrogen utilization efficiency under different fertilization management. The results showed that nitrogen fertilizer partial productivity (PFPN) decreased with the increase of nitrogen application. Compared with other treatments, the Shannon and Simpson indexes of the N treatment increased by 1.03 %-4.12 (p > 0.05) and 1.04 %-3.13 % (p > 0.05), respectively, and the Chao1 index increased by 3.31 %-9.37 % (p > 0.05), which did not achieve significant difference. The abundance of nitrogen cycle dominant bacteria treated with organic fertilizer increased by 17.65 %-37.68 % (p < 0.05). This study also selected 23 genes involved in assimilation nitrate reduction, dissimilatory ammonia nitrate reduction, nitrification, denitrification pathway. Compared with that of other treatments, M2N of assimilation nitrate reduction genes increased by 10.92 %- 47.07 %, in which, except for N treatment, there was no significant difference between other treatments. Denitrification reaction genes increased by 44.84 %-56.74 % (p < 0.05), which showed no significant difference between treatments N and M2N. Treatment M and M1N have great similarity in the functional gene composition of the nitrogen cycle, mainly pmoC-amoC and nirB in nitrification and dissimilatory ammonia nitrate reduction, while treatment N and M2N showed great similarity, mainly affected by denitrification and assimilation nitrate reduction, and the main affected genes were nirK and nasA. To sum up, the addition of organic fertilizer reduced the dissimilatory ammonia nitrate and nitrification related gene abundance, increased the assimilation nitrate and denitrification related gene abundance. Fertilization amount and species affected PFPN mainly through influencing microbial species richness and nitrogen cycle-dominant pathway. This study could provide theoretical basis for formulating scientific and reasonable fertilization strategies in arid regions from the perspective of soil microorganisms.