The ability of Elsholtzia splendens Naki( E. splendens) to accumulate copper appears to be governed by its high degree of copper tolerance. However, the tolerance mechanism on the physiological basis is unknown. Using transmission electron microscope (TEM) and energy dispersive analysis of X-rays(EDX), the likely location of copper within the cells of the tolerant and non-tolerant was determined. Here the role of vacuolar and cell wall compartmentalization in this copper tolerant plant were investigated. A direct comparison of copper locations of E. splendens and the non-tolerant Astragalus sinicus L. ( A. sinicus) showed that the majority of copper in the tolerant was localized primarily in the vacuolar, cell wall, on the plasmamembrane, beside lipid grains induced by copper pollution, in the chloroplasts and amyloids; but in the non-tolerant, copper precipitates only be observed on the plasmamembrane, in the chloroplasts and cytoplasm under copper exposure conditions that were toxic to both species. This revealed that the tolerant accumulates more copper in the vacuole and cell wall than the non-tolerant, where was regarded as the storage compartment of tolerant plant or hyperaccumulator for heavy metals.