Tropical cyclone (TC) intensification over marginal seas, especially rapid intensification (RI), often poses great threat to lives and properties in coastal regions and is subject to large forecast errors. It is thus important to understand the characteristics of TC intensification and the involved key factors affecting TC intensification over marginal seas. In this study, the 6-hourly TC best-track data from Shanghai Typhoon Institute of China Meteorological Administration, ERA-Interim reanalysis data, and TRMM satellite rainfall products are used to analyze and compare the climatological characteristics and key factors of different intensification stratifications over the marginal seas of China (MSC) and the western North Pacific (WNP) during 1980–2018. The statistical results show that TC intensification over the MSC is more likely to occur when TCs experience relatively large intensities, weak vertical wind shear, small translation perpendicular to the coastline, relatively high fullness, strong upper-level divergence, low-level relative vorticity, and high inner-core precipitation rate. The box difference index method is used to quantify the relative contributions of these factors to TC RI. Results show that the initial (relative) intensity contributes the most to TC RI over both the MSC and the WNP. The inner-core precipitation rate and translation perpendicular to the coastline are of second importance to TC RI over the MSC, while both vertical wind shear and TC fullness are crucial to TC RI over the WNP. These findings may help understand TC activity over the MSC and provide a basis for improving intensity prediction of TCs in the MSC.