Biogenic elements are the basis of primary production in marine systems. Their cycles in marine environments are affected by various physical, chemical, and biological processes. Understanding the concentration distribution, structural characteristics, and influencing factors of biogenic elements are essential to understand the dynamics of marine ecosystems. In February 2019, a field investigation was conducted in the Shenhu Area of the northern South China Sea and seawater samples were collected to analyze dissolved inorganic nutrients. Combined with the hydrological environment parameters, such as temperature, salinity, chlrophyll a (Chl a), pH and dissolved oxygen (DO), the distribution and controlling factor of nutrient concentration and structure in the Shenhu Area were discussed. Concentrations of each nutrient in the seawaters from 0 m to 30 m were very low, and the nutrient concentrations gradually increased with the increase of depth. At the depth of about 3 000 m, the concentrations of dissolved inorganic nitrogen (DIN), phosphate and silicate reached 38.02 μmol/L, 2.71 μmol/L and 149.07 μmol/L, respectively. Temperature, pH and DO were significantly correlated with nutrients, indicating that environmental factors greatly affected the biogeochemical processes of nutrients. In addition, the concentration of nutrients in the northeast direction of the study area at a depth of 75 m was relatively low and showed a gradual increasing trend in the southwest direction, which may be related to the intrusion of Kuroshio water with high temperature, high salinity and low nutrients. Meanwhile, the difference between the conservative mixing concentrations calculated based on an end-member mixing model and the measured values of nutrients showed that, at 75 m depth, silicate and phosphate were consumed by biological activities, while nitrates were controlled by biological addition. With the increase of phosphate, the DIN at each site increased linearly, but the silicate increased with a power function, indicating that the regeneration rate and recycling efficiency were different for different nutrients. The ratios of N/P in the Shenhu Area showed opposite trends compared with the ratios of Si/N and Si/P. At 0−30 m, the N/P ratios were low and the Si/N and Si/P ratios were high. At 75 m, the N/P ratios increased along with the decrease of Si/N and Si/P ratios possibly because of different biological effects. Below 75 m, the N/P ratios gradually decreased to 14.44, while the Si/N and Si/P ratios gradually increased. All nutrient ratios remained stable below 1 000 m. The calculation results of the N−anomaly showed that nitrogen fixation in seawater above 300 m was stronger than denitrification, and denitrification below 300 m was enhanced. The distribution characteristics of the concentration and structure of nutrients in the Shenhu Area indicated that the Kuroshio intrusion and biological activities significantly affected the biogeochemical process of nutrients in this area.