Marine microplastic (MP) pollution is a global environmental problem that has received attention from scientific researchers and the public for the past several decades. However, without a suitably large-volume sampling method, the presence of MPs in subsurface water (< 5 m) is poorly understood. Here, MP content in subsurface water was determined using a pump-underway ship intake system along the cross-oceanic transect from the Pearl River Estuary to the Indian Ocean. The study regions have always been considered as one of the major MPs hotspots in the global oceans and still lack of study. Generally, MP abundance ranged between 0 and 4.97 items m^-3, with an overall mean value of 0.40 ± 0.62 items m^-3. A total of 679 MP particles were identified using μ-FT-IR. These collections identified polyethylene (PE), polypropylene (PP), and polyester (PET) as the major polymers represented (73.14–88.81%). The presence of MPs in coastal regions was significantly higher than that in the open ocean, revealing the contribution of land-based sources to marine MPs and the ocean dynamics. Therefore, an effective and feasible way to retard the penetration of MPs into the marine environment is to exhibit controls at the source. No significant correlation was found between the MP abundance and the physical and chemical properties of water. The results of the analysis of similarities (ANOSIM) and non-metric multidimensional scaling (NMDS) also showed that MP communities in different environments were significantly greater than the differences in different sites within the same environment. These findings of this study provide reliable information on MP distribution and characterization in cross-oceanic region of South China Sea and Eastern Indian Ocean, which will help to improve our understanding about the fate of MPs in the ocean.