Using metagenome sequencing technology and fixed carbon and nitrogen metabolism in KEGG database as a research tool, taking wheat continuous cropping grain longterm positioning of three methods for fertilizing soil in Shaanxi Weihe Hanyuan as the research object, the influence of microbes in the farmland ecosystem in the region of fixed carbon and nitrogen metabolism pathway of main microbial species and functional genes were analyzed, and the results were as follows: PcoA analysis of metabolic pathways of soil microorganisms at KEGG database Level 3 at three fertilization levels showed that the abundance of functional genes in soil under conventional fertilization was closely related to the balanced fertilization treatment, but it was far from that under low fertilization. Fertilization significantly changed the functional gene abundance of carbon fixation and nitrogen metabolism, and the main functional genes of conventional fertilization and balanced fertilization were larger than that of lowdose fertilization. In the carbon fixation pathway, the abundance of main functional genes in the conventional fertilization was greater than that in the balanced fertilization, and in the nitrogen metabolism pathway, the abundance of the main functional genes in the balanced fertilization was greater than that in the conventional fertilization. Sorangium, Spiribacter, Lentzea, Rhodovibrio, Pseudomonas, Flavihumibacter, Streptomyces, Nitrososphaera, Rubrobacter, Dyadobacter, Novosphingobium, Pedosphaera, Thermogemmatispora were population of soil carbon fixation pathway marker microorganisms in this region. E4212A.fumA.fumB, E2319.atoB, mdh, ACSS.acs, korB.oorB.oforB, pps.ppsA, ppdK, sdhA.frdA, K18594, K18604, E4212 B.fumC, folD, ppc and accA produced significant responses to carbon fixation function genes for fertilization level. Sphingopyxis, Alcanivorax, Nitrosospira, Aeromicrobium, Roseiflexus, Devosia, Altererythrobacter were major species of nitrogen metabolism. nirB, nasA, nasB, nrt.nak.nrtP.nasA and GDH2 were the main functional genes of nitrogen metabolism in this region. Balanced fertilization was more beneficial to fertilizer saving and emission reduction and sustainable use of soil, which was the fertilization level suitable for continuous wheat field in this region.