The Karimata Strait (KS) throughflow between the South China Sea (SCS) and Java Sea plays an essential role in heat and freshwater budget in the SCS and dual roles in strengthening/reducing the primary Indonesian throughflow (ITF) in the Makassar Strait. A sustained long-term monitoring of the ITF is logistically challenging and expensive; therefore, proxies are needed. Here, we use a combination of in situ measurement of the KS throughflow and satellite-derived sea surface height (SSH) and sea surface wind (SSW) to determine the interannual and decadal modulations in seasonal amplitude of the KS throughflow associated with El Niño-Southern Oscillation (ENSO), Indian Ocean dipole (IOD), Pacific Decadal Oscillation (PDO). Linear regression, correlation, harmonic and power spectrum analyses are used. The results manifest that there are significant interannual to decadal modulations in the seasonal amplitude of the KS throughflow. The modulations of the seasonal amplitude in the volume and heat transports range 1.36-1.92 Sv (1 Sv = 106 m3 s-1) and 126.41-173.36 TW (1 TW = 1012 W), respectively, with a significant cycle of ~9 years. From 1994 to 2020, the seasonal amplitude of volume transport through the KS shows an increasing trend of 37.75 ± 15.69 mSv decade-1 (1 mSv = 103 m3 s-1). The seasonal amplitude of the heat transport also increases, at a rate of 4.78 ± 1.52 TW decade-1. The KS volume transport is positively correlated with PDO and ENSO indices (r2 = 0.69 and r2 = 0.58), with a lag of 12 and 10 months, respectively. The results of composite analysis suggest that the interannual variability of the KS transport is related to the interannual anomalies of the SSH gradient and the local SSW fields in boreal winter.