Using satellite altimetry sea surface height anomalies (SSHA) and Argo profiles, we investigated eddy’s statistical characteristics, 3-D structures, eddy-induced physical parameter changes, and heat/freshwater transports in the South China Sea (SCS). In total, 31,744 cyclonic eddies (CEs, snapshot) and 29,324 anticyclonic eddies (AEs) were detected in the SCS between 1 January 2005 and 31 December 2016. The composite analysis has uncovered that changes in physical parameters modulated by eddies are mainly confined to the upper 400 m. The maximum change of temperature (T), salinity (S) and potential density (σ_θ) within the composite CE reaches −1.5 °C at about 70 m, 0.1 psu at about 50 m, and 0.5 kg m⁻³ at about 60 m, respectively. In contrast, the maximum change of T, S and σ_θ in the composite AE reaches 1.6 °C (about 110 m), −0.1 psu (about 70 m), and −0.5 kg m⁻³ (about 90 m), respectively. The maximum swirl velocity within the composite CE and AE reaches 0.3 m s⁻¹. The zonal freshwater transport induced by CEs and AEs is (373.6 ± 9.7)×10³ m³ s⁻¹ and (384.2 ± 10.8)×10³ m³ s⁻¹, respectively, contributing up to (8.5 ± 0.2)% and (8.7 ± 0.2)% of the annual mean transport through the Luzon Strait.