<p>The Savu Sea, a key region for bidirectional water exchange between the Indian and Pacific Oceans, is influenced by monsoons, oceanic processes and climatic events. Its complex dynamics and ecological importance make it a critical region for studying the multiscale spatiotemporal variations of particulate organic carbon (POC). However, POC in this region remains poorly studied. Based on remote sensing POC data and multi-source environmental variables (2003–2021), this study reveals the spatiotemporal distribution and controlling mechanisms of POC in the Savu Sea. The results show that POC concentrations exhibit spatiotemporal variability. Spatially, the upwelling-influenced eastern coast exhibits the highest POC variability, while the Ombai Strait, dominated by the Indonesian Throughflow, shows the lowest POC and weakest variability. Seasonally, POC peaks during the southeast monsoon (May–October) due to coastal upwelling and cyclonic eddies. During the westerly monsoon (November–April), warm surface water and increased precipitation suppress upwelling, reducing POC. On interannual timescales, positive POC anomalies during El Niño and + IOD events, and negative anomalies during La Niña and -IOD, are mediated by Rossby and Kelvin waves that shoal the thermocline, enhancing upwelling and nutrient supply for phytoplankton growth. These responses lag ENSO by 3–5 months and IOD by ~ 1 month. Notably, the positive POC anomaly in 2011 was particularly pronounced, triggered by strong cyclonic eddy that enhanced local nutrient supply and productivity. Overall, this study demonstrates how multiscale processes control POC variability in the Savu Sea, offering new insights into carbon cycling and climate feedbacks in tropical marginal seas.</p>