Abstract: In this paper, a comprehensive evaluation method of new crop varieties in regional test based on multi-objective relational analysis is presented. The method not only estimated the value of crop varieties impersonally, but also debased the difficulty of comprehensive evaluation method on Regional test evidently. This paper provided a means to make a decision scientifically for the department on breeding, research and popularize. The author gave an effective new analysis method for the superior factor analysis of biology system and the comprehensive evaluation of single factor experimentation.