Long-term continuous cropping of facility soils could influence soil properties, however, the differences in soil properties among different continuous cropping years are still not well understood. The objective of this study was to explore the effects of continuous cropping years of lily on the physical and chemical properties and biological characteristics of facility red soil under subtropical conditions. The real-time fluorescent quantitative PCR, chloroform fumigation culture method, fluorescein diacetate (FDA), and other methods were used to examine the changes of the number of bacteria and fungi in the soil, the abundance of nitrogen (N) conversion functional genes, microbial biomass carbon (MBC) and nitrogen (MBN), and total microbial enzyme activities in facility red soil after continuous Lily cropping for 4 years, 5 years, 7 years. As the continuous Lily cropping years increased, soil pH decreased, and soil available nutrients and organic matter accumulated. The number of bacteria and the nirS gene abundance of denitrifying bacteria were the lowest in continuous cropping for 4 years and the highest after 7 years of continuous cropping. The number of fungi and the nirK gene of denitrifying bacteria rose. Compared with the control with no Lily grown, the copy number of AOA gene in the facility soil after 4 years, 5 years, and 7 years of continuous cropping decreased by 99.5%, 73.8%, and 45.2%, respectively; however, the AOB gene copy number increased by 51.1%, 79.1%, and 112.4%, respectively. The copy number of the N-fixing gene nifH decreased significantly and the MBC and MBN contents increased significantly. The total enzyme activity of microorganisms showed a trend of increasing first and then decreasing with the extension of continuous cropping years and reached the maximum value at 5 years of continuous cropping. As continuous cropping years increased, the total enzyme activity increased with continuous cropping for 5 years, and then showed a downward trend. The key factor affecting soil microbial activity was continuous cropping years. The results of this study lay the foundation for future research on the influence of continuous cropping years on the health of facility soil.