Biological agriculture, a new model utilizing modern biotechnology to enhance the production efficiency and sustainability of traditional agriculture, is both a strategic high ground in international agricultural competition and a crucial sector for China’s bioeconomy. In recent years, modern biotechnological approaches such as genetic engineering, protein engineering, enzyme engineering fermentation engineering, and synthetic biotechnology have made certain progress in developing new varieties of high-yield, quality-efficient, and environmentally friendly fertilizers, healthy and green feed, as well as safe pesticides with little residue. In the future, there are five major challenges and opportunities facing the development of biological agriculture, namely, constant expansion of the field of agricultural biology, the increasing importance of common technologies, platforms, and applications across plants and animals, the increasing importance of Big Data and AI, and increasingly intense international competition and biosecurity issues.