Due to the unique optical properties and excellent biological applications, carbon-based luminescent materials have become a research hotspot in recent years. In this paper, we report a synthesis method under mild condition, in which Carbon NanoCrystals (CNCs) were first prepared, and then high-purity multi-color carbon dots (HPMCCDs) were synthesized by modulating crystal morphology. The prepared nonfluorescent CNCs are, respectively, dissolved in a strong polar solvent and a weak polar solvent to prepare HPMCCDs. It exhibits the multi-excitation and multi-emission features (from green to yellow). The high-purity carbon dots (HPCDs) prepared by using this method demonstrate the higher quantum yields (QYs) (53.7%) than that of the carbon dots (CD) by traditional hydrothermal methods with dialysis, and make full use of the atomic economic model. Besides, it shows the unique up-conversion luminescence property (UCLP) at lower wavelength excitation and, which can also be placed for a long time at room temperature without being oxidized or deteriorated. Furthermore, we explored the regulation of polar-chromism mechanism of the CNCs. Finally, the HPMCCDs can be used for multi-color bioimaging in vivo and in vitro and as well as many other potential applications.