In this paper, the theory of heterosis controlled by core traits (genes) was put forward. Growth period traits and stem type traits were two core traits of heterosis in crops. However, due to the low yield of early-maturing parents, although the relative advantage was high, the absolute yield level of heterosis in the F1 generation was not necessarily high. Because seed production requires that the difference between two parents’ growth periods should not be very big, it also limited the potential of using gene interaction of growth periods to improve heterosis. In addition, the genes that control the growth period also included the genes that control each growth stage, so that the genes that control the growth period were not many, but not very few, because there were more genes that disperse and weaken the action intensity of major genes and increasing heterosis of the F1 generation was difficult. The genes controlling different stem types were all single. When the maturity of two parents is the same or similar, the combinations with different stem types got the maximum heterosis of grain yield, and the F1 absolute yield level is also the highest. Therefore, in heterosis utilization breeding, the differences of stem types should be mainly used and differences of growth periods should be properly used. Mechanism and root producing heterosis of crops were that strong interaction of major genes among different types of the most important quality traits (ecological traits) lead to great improvement in the vitality of all quantitative traits. Growing period and Stem type were two nucleus traits producing heterosis of crops. Therefore this theory was called as core trait theory producing heterosis of crops.