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As the environmental nuclear radiation pollution caused by nuclear-contaminated water discharge and other factors intensifies, more plant–microorganism–soil systems will be under long-term low-dose ionizing radiation (LLR). However, the regulatory mechanisms of the plant–microorganism–soil system under LLR are still unclear. In this study, we study a system that has been stably exposed to low-dose ionizing radiation for 10 years and investigate the response of the plant–microorganism–soil system to LLR based on the decay of the absorbed dose rate with distance. The results show that LLR affects the carbon and nitrogen migration process between plant–microorganism–soil through the “symbiotic microbial effect.” The increase in the intensity of ionizing radiation led to a significant increase in the relative abundance of symbiotic fungi, such as Ectomycorrhizal fungi and Rhizobiales, which is accompanied by a significant increase in soil lignin peroxidase (LiP) activity, the C/N ratio, and C%. Meanwhile, enhanced radiation intensity causes adaptive changes in the plant functional traits. This study demonstrates that the “symbiotic microbial effect” of plant–microorganism–soil systems is an important process in terrestrial ecosystems in response to LLR.