Mesoscale eddies are very active in the Northwestern Pacific. They continuously propagate westward and eventually meet the strong western boundary current (Kuroshio) east of the Luzon and Taiwan islands. When the mesoscale eddies interact with the Kuroshio, the speed and path of the Kuroshio are significantly changed, their three-dimensional structures were changed, and ultimately dissipated. At present, there have been many studies on the evolution of mesoscale eddies east of the Taiwan Island, but the evolution process of mesoscale eddies east of the Luzon Island and the similarities and differences with those east of the Taiwan Island remain unclear. Based on the satellite altimeter data from 1993 to 2019 and OFES (Ocean General Circulation Model for the Earth Simulator) model data with a resolution of 1/10° ×1/10°, we compared and analyzed the three-dimensional evolution processes of mesoscale eddies originating from the inner Pacific Ocean when they propagate westwards and meet the Kuroshio east of the Luzon and Taiwan islands. Results show that the mesoscale eddies in the two islands regions underwent four stages: contact, deformation, stretching, and dissipation. In general, the mesoscale eddies east of the Taiwan Island are stronger and have a longer interaction period with the Kuroshio. The interaction time of cyclonic (anticyclonic) eddies with the Kuroshio east of the Taiwan (Luzon) Island is 39 (33) and 54 (24) days, indicating that the cyclonic eddies (anticyclonic eddies) east of the Taiwan (Luzon) Island decay faster. In horizontal direction, after meeting the Kuroshio east of Taiwan, the mesoscale eddies gradually deformed into inclined ellipses in the NE-SW direction. However, the mesoscale eddies are mainly stretched in the N-S direction when they encounter the Kuroshio east of the Luzon Island. In vertical direction, the centers of cyclonic (anticyclonic) eddies east of the Taiwan Island inclined southwestward (northwestward) with increasing depth, and the degree of inclination gradually decreased over time, whereas the vertical inclination of the mesoscale eddies east of the Luzon Island was not significant. Besides, in both islands regions, cyclonic (anticyclonic) eddies lead to a weakening (strengthening) of the Kuroshio. Due to the blocking effect of the Kuroshio’s jet, the mesoscale eddies caused seesaw-like variations in sea surface height and sub-surface temperature in the two sides of the Kuroshio.