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This study investigates long‐term sea level changes in the South China Sea (SCS) using a validated high‐resolution regional ocean model simulation for the Maritime Continent. The contributions of ocean mass redistribution and steric sea level are examined to understand the sea level variations. The ocean bottom pressure (OBP) serves as an indicator of sea level variations linked to alterations in ocean mass flux. The OBP accounts for over 80% of the total sea level change over the shelves, while the steric sea level emerges as the dominant factor, contributing over 50% to the sea level change in the deep SCS. Luzon Strait transport shows a weakening trend in the last six decades, resulting in higher heat accumulation and larger steric expansion in the deep SCS. The ocean mass redistribution acts as a mechanism to balance the contrasting steric induced sea level changes over the deep SCS and shallow continental shelves. Plain Language Summary: The South China Sea (SCS) has vast continental shelves covering more than half of its surface area. The study investigates long‐term sea level changes in the SCS using an ocean general circulation model simulation, considering steric sea level (water expansion due to temperature and salinity changes) and ocean mass redistribution. The analysis showed a significant increase in steric sea level in the deep SCS, while the contribution of ocean mass redistribution decreased. The mass redistribution was responsible for over 80% of the total sea level change, except in the deep SCS, where steric sea level dominated. Weakened flow from the Pacific Ocean to the SCS led to more heat accumulation and higher steric expansion in the deep SCS, causing water to redistribute toward the shelves. Key Points: About 80% of the sea level changes over the South China Sea (SCS) shelves are attributed to the redistribution of ocean mass from deeper regionsThe SCS throughflow has exhibited a weakening trend over the past six decadesSteric sea level changes, driven by fluctuations in Luzon Strait transport, dominate long‐term sea level variations in the SCS [ABSTRACT FROM AUTHOR]