The seasonal to interannual variability of eddy kinetic energy (EKE) in the Northeastern South China Sea (NE-SCS) has been widely studied and it is recognized that they are strongly related to the state of the Kuroshio pathway in the Luzon Strait. While, due to the lack of long-term observations and high-resolution simulations, the decadal change of EKE in NE-SCS remains unexplored. In this study, we show the EKE trend in the past ∼ 30 years in the NE-SCS by using satellite observation and global HYbrid Coordinate Ocean Model reanalysis with the Navy Coupled Ocean Data Assimilation. It is found that due to the weakening of the Kuroshio in the Luzon Strait since 1990 s, the Kuroshio shows an enhanced looping path in the NE-SCS, inducing stronger EKE in this region. Further analysis confirms that the energy transfer by baroclinic instability is dominant for the increasing of EKE, when the Kuroshio intrudes into the NE-SCS and brings more potential energy inside the circulation. The Kuroshio state along the Luzon Strait is the key for modulating the EKE in the NE-SCS. Furthermore, the long-term weakening of Kuroshio current along the Luzon strait during 1993–2020 is determined by the decreasing of subtropical mode water, corresponding to the positive phase of the Atlantic Multidecadal Oscillation. This study provides insight into the interaction between marginal sea (i.e., the SCS) and the open ocean (i.e., the western Pacific Ocean), finally linking to the global climate change.