Haptophytes (Eukaryota, Hacrobia) play a crucial role in the energy budget and element cycling of diverse aquatic ecosystems due to their ability to engage in both phototrophic and mixotrophic nutritional modes. Nevertheless, there is a significant lack of knowledge regarding the short-term variations, such as diel dynamics, of their ecological features. During a short time frame in the summer of 2018, samples were collected from three distinct water layers in the South China Sea, including surface water, the deep chlorophyll maximum (DCM) layer, and 200m depth. Fluorescence in situ hybridization coupled with tyramide signal amplification was used to quantify haptophyte cell abundance. Most haptophyte communities in all three water layers were composed of cells 2–5µm in size, while the proportion of cells <2µm increased with water depth. High-throughput sequencing of the V4 hypervariable regions of the SSU rRNA revealed that Chrysochromulina and Phaeocystis predominated the community, and the former was more abundant in the surface water and 200m depth and the latter was more abundant in the DCM layer. Higher abundance of small cells (<2µm and 2–5µm) during the night was found compared to the day time, whereas large cells (5–10µm and 10–20µm) were more prevalent during the day time. The results of correlation analyses showed that haptophyte abundance was possibly impacted by both environmental biotic (heterotrophic nanoflagellates, heterotrophic bacteria, and viruses) and abiotic (temperature, salinity, and nutrients) factors.