Mesoscale eddies play vital roles in ocean processes. Although previous studies focused on eddy surface features and individual three-dimensional (3D) eddy cases in the northwestern Pacific Ocean, the analysis of unique eddy 3D regional characteristics is still lacking. A 3D eddy detection scheme is applied to 9 years (2000–2008) of eddy-resolving Regional Ocean Modeling System (ROMS) output to obtain a 3D eddy dataset from the surface to a depth of 1 000 m in the northwestern Pacific Ocean (15°–35°N and 120°–145°E). The 3D characteristics of mesoscale eddies are analyzed in two regions, namely, Box1 (Subtropical Countercurrent, 15°–25°N and 120°–145°E) and Box2 (Southern Kuroshio Extension, 25°–35°N and 120°–145°E). In Box1, the current is characterized by strong vertical shear and weak horizontal shear. In Box2, the current is characterized by the strong Kuroshio, topographic effect, and the westward propagation of Rossby waves. The results indicate the importance of baroclinic instability in Box1, whereas in Box2, both the barotropic and baroclinic instability are important. Moreover, the mesoscale eddies’ properties in Box1 and Box2 are distinct. The eddies in Box1 have larger number and radius but a shorter lifetime. By contrast, Box2 has fewer eddies, which have smaller radius but longer lifetime. Vertically, more eddies are detected at the subsurface than at the surface in both regions; the depth of 650 m is the turning point in Box1. Above this depth, the number of cyclonic eddy (CE)s is larger than that of anticyclonic eddy (AE)s. In Box2, the number of CEs is dominant vertically. Eddy kinetic energy (EKE) and mean normalized relative vorticity in Box2 are significantly higher than those in Box1. With increasing depth, the attenuation trend of EKE and relative vorticity of Box1 become greater than those of Box2. Furthermore, the upper ocean (about 300 m in depth) contains 68.6% of the eddies (instantaneous eddy). Only 16.6% of the eddies extend to 1 000 m. In addition, about 87% of the eddies are bowl-shaped eddies in the two regions. Only about 3% are cone-shaped eddies. With increasing depth of the eddies, the proportion of bowl-shaped eddies gradually decreases. Conversely, the cone- and lens-shaped eddies are equal in number at 700–1 000 m, accounting for about 30% each. Studying the 3D characteristics of eddies in two different regions of the northwestern Pacific Ocean is an important stepping stone for discussing the different eddy generation mechanisms.