Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. We cloned two major QTLs Ghd7 and Ghd8, with pleiotropic effects on grain yield, plant height and heading date in rice. They individually increases grain yield per plant up to 40-50% in near isogenic background. Ghd7 delays the heading date by regulating the flowering pathway mediated by Ehd1. Association mapping showed that the C/T mutation in the promoter region of Ghd7 contributes to all the three traits’ variation. Ghd8 encodes the OsHAP3 subunit of a CCAAT-box binding protein (HAP complex). By regulating Ehd1, RFT1, and Hd3a, Ghd8 delays flowering under long-day conditions, but promoted flowering under short-day conditions. For the both QTLs, several weak, strong or no functional alleles are distributed to different ecotypes. Ghd7 genetically interacts with Ghd8, which strongly delays the heading date and significantly increases the number of spikelets per panicle under long day condition. However, Ghd7 and Ghd8 interaction effects depend on its genetic background. Overall, Ghd7 and Ghd8 provide us a precious opportunity for studying the molecular mechanism of the association between grain yield and heading. Characterization of such mechanisms will lead to a series of discoveries of fundamental importance in plant biology.