The driving mechanisms of mesoscale processes and associated heat transport in the Japan/East Sea (JES) from 1990 to 2010 were examined using eddy-resolving ocean model simulations. The simulated circulation showed correctly reproduced JES major basin-scale currents and mesoscale dynamics features. We show that mesoscale eddies can deepen isotherms/isohalines up to several hundred meters and transport warm and low salinity waters along the western and eastern JES boundaries. The analysis of eddy kinetic energy (EKE) showed that the mesoscale dynamics reaches a maximum intensity in the upper 300 m layer. Throughout the year, the EKE maximum is observed in the southeastern JES, and a pronounced seasonal variability is observed in the southwestern and northwestern JES. The comparison of the EKE budget components confirmed that various mechanisms can be responsible for the generation of mesoscale dynamics during the year. From winter to spring, the baroclinic instability of basin-scale currents is the leading mechanism of the JES mesoscale dynamics’ generation. In summer, the leading role in the generation of the mesoscale dynamics is played by the barotropic instability of basin-scale currents, which are responsible for the emergence of mesoscale eddies, and in autumn, the leading role is played by instabilities and the eddy wind work. We show that the meridional heat transport (MHT) is mainly polewards. Furthermore, we reveal two paths of eddy heat transport across the Subpolar Front: along the western and eastern (along 138∘ E) JES boundaries. Near the Tsugaru Strait, we describe the detected intensive westward eddy heat transport reaching its maximum in the first half of the year and decreasing to the minimum by summer.