An atrazine-degrading strain HB-5 was used as a bacteria for biodegradation. Treatments of soil with nitrogen single, phosphate single and nitrogen phosphate together with HB-5 were carried out for degradation and eco-toxicity test; then, relationship between atrazine degradation rate and soil available nitrogen, available phosphorus were discussed. Atrazine residues were determined by HPLC; available nitrogen was determined with alkaline hydrolysis diffusion method; available phosphorus was determined with 0.5 mol/L-NaHCO3 extraction and molybdenum stibium anti-color method, and toxicity test was carried out with micronucleus test of Vicia faba root tip cells. The results showed that: After separately or together application, nitrogenous and phosphorous fertilizers could significantly accelerate atrazine degradation than soil with HB-5 only. On day 5, the order of atrazine degradation was ANP>> AP>> AN>> A; 7 days later, no statistically significant differences were found between treatments. The available nitrogen and phosphorus level in soil reduced as the degradation rate increased in the soil. The soil of eco-toxicity test results indicated that the eco-toxicity significantly reduced with the degradation of atrazine by HB-5, and the eco-toxicity on treatments of soil with fertilizer were all below the treatments without fertilizer. On day 5, the order of eco-toxicity was ANP < AP < AN < A; 7 days later, all treatments were decreased in control levels. So, adjusting soil nutrient content could not only promote atrazine degradation in soil but also could reduce the soil eco-toxicity effects that atrazine caused. All these results could be keystone of atrazine pollution remediation in contaminated soil in the future.