Breeding technologies have made great contributions to the improvement of grain yield and quality in crops. The innovations of crop breeding benefit from the advances in genetics, molecular biology and genomics. To meet the challenge of increasing demands in crop production, it is urgent to develop a powerful, effective and precise system for breeding high-yield and good-quality elite varieties by rational design and targeted improvement of complex traits. The breakthrough in molecular design strategy largely depends on the elucidation of molecular mechanisms underlying high-yield and superior-quality traits. To break the bottleneck of rice grain yield and enhance rice yield potential over existing high-yield varieties, the concept of ideal plant architecture has been proposed, aiming to cultivate elite rice varieties with moderate tiller number, thick and sturdy stems, more grains per panicle than currently cultivated varieties, high grain quality, and eventually achieve so-called ‘New Green Revolution’. This project addressed the fundamental scientific question of ‘the molecular mechanism underlying ideal plant architecture and grain yield in rice’, characterized, created and utilized valuable germplasm resources in rice, and developed a series of algorithm for genome-wide associate analysis and precise detection of the genetic loci that control complex agronomic traits, innovating the genetic dissection of complex agronomic traits. This project characterized Ideal Plant Architecture 1 (IPA1) as a key regulator that defines rice plant architecture, systemically investigated the molecular basis of rice ideal plant architecture, and further enhanced rice grain yield through adoption of the beneficial IPA1 alleles in current high-yield varieties harboring the semi-dwarf gene. This project also systemically analyzed the regulatory network of rice cooking and eating quality, and provided important strategy and genetic resources for the improvement of rice quality by molecular design. They creatively established an efficient system of breeding by molecular design, succeed in breeding a series of new elite varieties with high-yield and good-quality, and developed an effective strategy to break the mutual restrictiveness between yield and quality in rice. These discoveries will play strong guiding roles in breeding crop varieties with high-yield and good-quality through molecular design. Their creative achievements are new breakthrough of the ‘Green Revolution’ and lay an important theoretical foundation for the ‘New Green Revolution’. They have published more than 120 papers in the top scientific journals, with more than 1000 impact factors and 8000 citations. The 8 representative papers have been cited more than 2300 times. Their original findings have important international influences and have been elected as “the Nation’s Top Ten Scientific Breakthroughs in China" in 2010 and 2014, respectively.