Abstract: Based on the shortage of the evaluation methods for soil quality, the artificial immune model was applied to evaluate soil quality. After analyzing the shortage of binary-encoding in the artificial immune model, the authors proposed to integrate DNA with immune algorithm and to construct an artificial immune model based on DNA-encoding. Then the new evaluation method was used to evaluate the soil quality in Dongguan Agricultural Modernization Experimental Field in Guangdong Province. The results showed the new evaluation method was stable and reliable. The artificial immune model based on DNA-encoding was able to solve the soil quality evaluation problems which were uncertain, fuzzy, and had a spatial characteristic. It was also able to solve the problem of multiple objects under multi-index condition for soil quality evaluation.