Abstract: Aquaponics is a kind of technology, which consists of a Recirculating Aquaculture System (RAS) and hydroponics, and uses aquaculture effluent to provide nutrients for plants. Agricultural products (fish and plants) are produced from one nitrogen source (fish feed), with such characteristics as energy and water conservation, and environmental friendliness, which makes it a sustainable way of agricultural development. In this paper, the research status of nitrogen and phosphorus utilization efficiency of aquaponics was discussed from three aspects: Operating process conditions, system design, and biological agents. This paper summarized the optimization effect and principle of the operating process conditions of the aquaponics system: the adjustment of pH, dissolved oxygen, and hydraulic loading, the improvement of feeding frequency and feeding strategy, plant selection, and precise planting ratio, which could affect the nitrogen and phosphorus utilization efficiency of the system by directly affecting the normal growth and biological yield of fish, plants, and microorganisms. The advantages and limitations of different planting patterns and system construction patterns in the design of aquaponics systems to improve the system nitrogen and phosphorus utilization efficiency were analyzed. Media bed culture had higher nitrogen utilization efficiency than deep-water culture and nutrient film pipeline culture due to its higher microbial load. The decoupling type had more development potential than the coupling type because of its more precise control conditions and more equipment integration. This paper also summarized the application prospect of biological agents including microorganism preparation, plant extracts, and algae in aquaponics systems: Which could be used as water quality improvement regulators or fed additives to improve nitrogen and phosphorus utilization efficiency of the system by decomposing residual bait of fish manure, increasing nitrification, promoting plant growth, increasing dissolved oxygen, enhancing fish immunity, promoting nitrifying bacteria growth, improving feed utilization rate and other functions. Three suggestions for optimizing the aquaponics system and further improving the utilization rate of nitrogen and phosphorus nutrients in the system were put forward: Accelerating the research and development of fishery intelligent aquaculture equipment technology, strengthening the research on the mechanism of nitrogen and phosphorus transformation rule of aquaponics system under different conditions, and deepening the application of biological agents in the aquaponics system.