Transmission electron microscope (TEM) and high resolution transmission electron microscope (HRTEM) analyses have been performed on omphacite from ultra-high pressure (UHP) eclogites at the locality of Shima, Dabie Mountains, China. TEM reveals that the microstructures consist dominantly of dislocation substructures, including free dislocations, loops, tiltwalls, dislocation tangles and subboundaries. They were produced by high-temperature ductile deformation, of which the main mechanism was dislocation creep. Antiphase domain (APD) boundaries are common planar defects; an age of 470±6 Ma for UHP eclogite formation has been obtained from the equiaxial size of APDs in ordered omphacites from Shima, coincident with ages given by single-zircon U-Pb dating (471±2 Ma). HRTEM reveals C2/c and P2/n space groups in different parts of one single omphacite crystal, and no exsolution is observed in the studied samples, which is attributed to rapid cooling. It is suggested that the UHP eclogites underwent a long period of annealing at high temperatures, followed by relatively rapid cooling. These data provide valuable information for the formation and exhumation mechanism of UHP eclogites in the Dabie high-pressure (HP) and UHP metamorphic belt.