Abstract: This paper deals with the genetic variation between different seed sources and between clones within the seed sources for cone yields for 6 years successively after the first generation clonal seed orchard of masson pine putting into production.The results show that the differences between seed sources and clones are important variation sources, and the latters’ effect surpasses those of the former ones.The heritabilities based on seed source and clone mean are found to be high.There exists great fluctuation of cone production between different years(i.e.possessing marked bumper and lean year).37%～49% of the total variation can be attributed to year effect.The contributions of clones to total cone production are related to the genetic composition of clonal seed orchards and production years. In the seed orchards composed of clones from different seed sources, the significant genotype by year interaction of cone yield is found and should be payed attention to.If clones of seed orchards are from the same seed sources, the genotype by year interaction is smaller and meaningless in practice. In order to manage the seed orchards well, all clones could be divided into 5 types, according to the cone outputs and genetic stabilities.