Rice is one of the world's most important crops, playing an important role in national food security. Considering the decrease of arable cultivated land, the development of social economy, and the environmental restrictions by climate change, it is important to cultivate high-yield and good quality elite varieties in rice. Plant architecture is one of the main factors that determine rice grain yield, which mainly includes tiller number, tiller angle, plant height, and panicle morphology. Over past decades, breeding practices have greatly increased rice grain yield with plant architecture improvement, and two significant achievements have been made due to dwarfism breeding through the application of green revolution gene sd1 and utilization of hybrid vigor with the development of hybrid rice. Thus, it is of great significance to reveal the molecular basis of rice plant architecture. Besides the grain yield, rice grain quality is another important goal for rice breeding, which is mainly influenced by nutritional value, cooking and eating properties, storage ability, and grain appearance. With the development of rice functional genomic research and modern biological technology, significant progresses have been made in understanding rice shoot architecture and grain quality, which in turn promotes the molecular design of rice elite varieties. In this review, we discuss the molecular basis of rice plant architecture, especially the key regulator IPA1 that encodes rice SQUAMOSA Promoter Binding Protein Like-14 (OsSPL14) and determines the ideal plant architecture traits including decrease tiller number, increase plant height and panicle branches. We then discuss the molecular basis of grain quality, especially the cooking and eating quality of rice, one major index of grain quality, which is determined by amylose content, gel consistency and gelatinization temperature. These three traits are regulated by a complex genetic network, and the elucidation of major regulatory genes provides important strategy for improving rice quality by molecular selection. At mean time, the development of new technologies has greatly accelerated the scientific researches on relate areas. Genome-wide association studies (GWAS) had been applied for the efficient utilization of the genetic information in various rice varieties in the dissection of complex traits and provided a fundamental resource of rice breeding. Meanwhile, the revolutionary CRISPR technology has greatly increased the efficiency in generating new genetic resources and benefitting molecular breeding by design. In the future, the application of important agronomical genes in molecular breeding by design and the broad popularization of new varieties will bring a new leap for agriculture production.