Oceanic currents redistribute nutrients, phytoplankton, and other biogenic materials, fundamentally shaping marine biodiversity and ecosystem functioning. Yet, the topology of fine-scale material transport remains poorly resolved due to limitations in high-resolution flow observations. Here, by constructing Lagrangian flow networks from the Surface Water and Ocean Topography (SWOT) observations, we analyze surface fine-scale transport features in the South China Sea in 2023. Compared with networks derived from conventional altimetry products, SWOT-derived networks identify more sinks, sources, and transport gateways at 2–10-day timescales and spatial scales below ∼60 km (90 km) in summer (winter). As such, SWOT resolves hydrodynamic provinces that remain invisible to conventional altimetry, revealing previously undetected corridors and barriers of surface exchange. This advantage also provides better dynamic explanations for complex phytoplankton community structures and evolution. Our results highlight SWOT's transformative capacity to improve the diagnosis and prediction of ocean material transport, opening new avenues for interdisciplinary oceanographic and ecological applications.