The study of the changes in the structure and quantity of the denitrifying microbial community in the protected vegetable crop field is crucial for evaluating the soil quality of long-term protected cultivation and improving the understanding of nitrogen conversion. In this study, quantitative fluorescent PCR was used, with the help of the Illumina Miseq high-throughput sequencing platform, aiming at the nosZ gene, to study the effects of protected cultivation plots 3 a, 5 a, and 7 a, and the outdoor cultivation plot (ck) on the structure and quantity of soil denitrifying microbial community. The results demonstrated that the abundance of nosZ gene in ck was significantly higher than the other treatments, and was 1.32, 1.45 and 1.69 times those of Group 3 a, 5 a and 7 a, respectively. As the cultivation year increased, the abundance of nosZ gene was decreased, and the α-diversity index was decreased. The Chao1 index and ACE index of ck were the highest. At the phylum level, the dominant group was Proteobacteria. While at the genus level, the dominant groups were Bradyrhizobium and Achromobacter. The relative abundances of Proteobacteria and Bradyrhizobium were decreased with the increase of protected cultivation time. The principal component analysis (PCA) results showed that the community structure of nosZ varied greatly with the increase of planting time. The community structures of Group 3 a and 5 a were similar, but the community structure of Group 7 a was very different from Group 3 a and 5 a. The soil available potassium (AK), ammonium nitrogen and nitrate nitrogen were the primary factors affecting the copy number, α-diversity and community structure of nosZ denitrifying microorganisms. As a conclusion, it can be seen that long-term cultivation of vegetable crops in a protected environment significantly reduced the copy number of nosZ denitrifying microorganisms and had a significant impact on the community structure.