Abstract: The key factor of the rice varieties that whether could be cultivated in native region was the rice varieties with broad genetic basis and far genetic distance, and it was also the basis of choice parent in crossing breeding. The method of multiple factor statistic analysis was often used to examine the genetic difference between varieties and understand the genetic distance between parents. The materials in this experiment were the varieties of main cultivated or new brought in yellow river irrigation areas of Ningxia in many years. The twelve main agronomic characters of twenty rice varieties were investigated, and twelve main characters which showed notability difference were used to principal components analysis. Common factors were separated from principal component and used to cluster analysis. The average number of main characters in every class was calculated, and every class variety characteristic was obtained. The result showed that the twelve main characters of twenty rice varieties could be classified into five principal components. Through cluster analysis, twenty rice varieties could be classified into four class after choose proper threshold according to genetic distance, showing near genetic distance and narrow genetic basis in twenty rice varieties, and most varieties of Ningxia was collected mainly in the fourth class. Therefore, when choosing the parents in intercross breeding in rice, the parents should be complemented to each other in the principal component, and another parent was selected in other class, and combining with grain quality of rice, the new variety with excellent agronomic characters and grain quality and high product was brought up. When improved one or two characters, one parent accord with the demands of breeding object, another parent may be chosen in other varieties not so far for genetic distance in each other.