The intraseasonal variability (ISV) associated with mesoscale eddies in the northern South China Sea has been significant. Comparing the intraseasonal variability of flow at different times helps to elucidate the influence of mesoscale eddies with various dynamic instability, therefore, this study analyzed the dynamic instability of mesoscale eddies in the spring of 2009 and 2020 in the northern South China Sea, to figure out the characteristics of intraseasonal variability. Based on mooring velocity data, it conducted kinetic spectral analysis, and the results demonstrated that the ISV with period of 10‒60 days in 2009 and the ISV with period of 30‒90 days in 2020 displayed a similar vertical feature, with strong intraseasonal signals primarily occurring in the upper layer above 200 m. Moreover, the ISV with period of 30‒90 days was the main intraseasonal component during the corresponding observation period. Lag-regression analysis and calculation of dynamic instability showed that the intraseasonal variation of spring 2009 was affected by fast-moving but weak surface mesoscale eddies, and the dynamic instability was modulated by baroclinic instability and barotropic instability. On the other hand, the intraseasonal variability in the spring of 2020 was influenced by strong baroclinic mesoscale eddies, which might trigger the occurrence of intraseasonal variability in the flow fields more rapidly through enhanced vertical shear of velocity. The findings of this study contribute to a deeper understanding of the impact mechanisms of mesoscale eddies on intraseasonal activities in the northern South China Sea, providing important references and a theoretical basis for ocean dynamics and climate research.