Studies of the diel pattern of variable nutrients in the oligotrophic surface waters are challenging because their ambient concentrations are typically below the detection limits of standard colormetric methods. Here we conducted a time series analysis of nutrients with approximately 3-hour intervals in the oligotrophic South China Sea (SCS) basin in June 2017 to explore the dynamics of nutrients and their underlying physical and biological controls. We observed remarkably large variations of the “average” nutrient concentrations in the euphotic zone (0-100 m). At station SEATS located in the northern basin of the SCS, the concentrations varied from 19 to 515 nM for soluble reactive phosphate (SRP), from 4 to 7583 nM for inorganic nitrogen (nitrate plus nitrite, N+N) and from 1.9 to 7.4 μM for silicate. The minimum level occurred, and subsequently increased to the maximum at 9:00 p.m. Integrating the concentrations in the upper 100 m of the water column, the nutrient inventories exhibited an identical pattern following the variations of nutrient concentrations, with the minimum (10 mmol m−2 for SRP, 91 mmol m−2 for N+N, 257 mmol m−2 for silicate) at about 12:30 p.m. and the maximum (23 mmol m−2 for SRP, 319 mmol m−2 for N+N, 402 mmol m−2 for silicate) at 9:00 p.m. These diel patterns suggested that phytoplankton uptake peaked in the daytime while remineralization of organic matter that releases nutrients was more significant during the nighttime. We found a similar diel pattern at a more oligotrophic site located in the southern basin of the SCS (Station SS1), but with lower concentrations and inventories, and smaller amplitudes. The difference in the amplitudes in diel variability are likely associated with the differing biological productivity and upward input fluxes from depth between the northern and southern basin of SCS.