Abstract: At present, there are many kinds of methods for the comprehensive evaluation of filtering algorithms in deep space exploration, but most of them have problems more or less because of their singleness. In this case, a set of index system that reflects the degree of the filtering algorithm was put forward,and the corresponding mathematical model for the algorithm was established. The data of deep space probe sampling points were calculated by the model, and then synthetically evaluated by the fuzzy grey clustering method. The proposed evaluation model combines the grey system theory with the fuzzy comprehensive evaluation method. The model overcomes the shortcomings when the two methods are used seperately, and improves the accuracy of the evaluation results. The evaluation results show that the evaluation model is more accurate, and reasonable, which can evaluate the filtering algorithm comprehensively.