To provide a natural foundation and regionalization framework for ecological monitoring, assessment, and mapping to support ecosystem-based management practices of natural resources, three levels of ecological zones were classified in Chinese seas and adjacent waters using top-down and step wise nesting. At the largest spatial scale, the Chinese seas and adjacent waters were classified into three first-level ecological zones according to latitudinal zones and geographic profiles. To incorporate the dimensionalities and mobility of the seas, 22 second-level ecological zones were classified according to changes in water depth and the distribution of large water masses, and 53 third-level ecological zones were further delineated according to the type of geomorphology and the distribution of water masses and currents. This study identifies dominant factors at different spatiotemporal scales and defines the physical geographical patterns and ecological characteristics in Chinese seas and adjacent waters in a readily understood manner and fills the gap in research on ecological zoning in China.