Rare earth (RE) ions-doped luminescent nanocrystals (NCs) with numerous unique advantages have attracted tremendous interest for the wide applications from science to engineering, yet suffering from the shortcoming of thermal quenching coming from surface organic ligands. We propose utilizing a facile acid-base reaction to remove surface organic ligands introduced choosing carboxylic acids as stabilizing agent and weaken thermal quenching. The results showed that the acid-base reaction displayed an outstanding cleaning effect. After acid-treatment, most surface organic ligands were removed, and there was no influence on crystal structure and morphology of as-prepared beta-NaYF4:Er3+ NCs. Meanwhile, with no surface organic ligands capping, beta-NaYF4:Er3+ NCs preferred brighter emission after thermal treatment, including up-conversion (UC), near-infrared (NIR), and mid-infrared (MIR) emission. When calcined the acid-treated beta-NaYF4:Er3+ NCs in different atmosphere, such as oxygen and reducing atmosphere (15%H-2 + 85%N-2), an unexpected enhancement of all emission bands in Er3+ was determined under phase transformation temperature, especially in oxygen atmosphere. Furthermore, all the fluorescence lifetimes of Er3+ also exhibited obvious extension. Our results supposed that the beta-NaYF4:Er3+ NCs have promising applications in safety ink, and the acid-treatment by diluted hydrochloric acid is a general approach to remove deleterious organic ligands on NC surface further to weaken thermal quenching.