A soil fertility fuzzy evaluation model based on the contribution of microorganism was proposed. The microorganism kinetics were used to analyze the direct and indirect ecological effect on the soil fertility. The contribution of the microorganism was converted to the available nutrient element on the basis of the original non-biological evaluation index weight structure to calculate the weights which the traditional method was difficult to determine. The evaluating grade of the whole factors was divided and the appropriate membership function parameters were determined. The soil fertility fuzzy evaluation model was established. According to the correlation analysis between the evaluation results and the crop productions, it was showed that the correlation coefficient of the evaluation was higher than the traditional methods, which was more reasonable than the other evaluations.