To elucidate the pollution status and spatial distribution patterns of microplastics in representative deep-sea regions of China, the Qiongdongnan sea area has emerged as a key focus area for microplastic research. A comprehensive assessment of microplastic contamination across the water column (0–1500 m) was conducted using CTD-integrated water sampling coupled with 0.2 μm membrane filtration. Results revealed that polypropylene (PP), polyethylene (PE), and polyamide (PA) were the dominant polymer types. Granular microplastics constituted the overwhelming majority (95.3%) of identified particles, while size analysis showed that those in the 20–50 μm range accounted for the largest fraction (80.5%). The average microplastic abundance across all sampled depths was 3.47 particles/L. Comparative analysis with other prominent marine environments globally and domestically indicates minimal vertical differences in the characteristics of microplastics. Comparative analysis with other prominent marine environments globally and domestically indicates that microplastic pollution in the South China Sea is relatively moderate. This study delivers foundational empirical data critical for environmental risk assessment and source apportionment of microplastics in the South China Sea. This study provides key basic data for assessing the environmental risk of microplastics in the South China Sea and tracing their sources.