Zinc oxide nanoparticles (ZnO NPs) have unique physical and chemical properties and important application values in many fields, which has also been resulted the consequence that it was released into different environment, and increased the interaction with creatures, which is the most important aspect of the toxic effects of ZnO NPs. Aloe is a lily family of evergreen and fleshy herbs, which has important ornamental and medicinal value, Aloe-emodin (Aloe emodin, AE) is an important pigment molecule in aloe, which is also an important active ingredient of aloe as a medicinal plant. In this work, from a new perspective, the distribution of AE in leaves was investigated through the longitudinal slicing method with fluorescence microscopy, and which was comprehensively understood, and then the interaction between ZnO NPs and AE was studied. The changes of the color of AE and its fluorescence spectra under the influence of ZnO NPs were observed and analyzed. The results showed that the trend of the color change of AE solution was from light yellow through orange yellow, orange to orange red; moreover, compared with the control group, the ZnO NPs accelerate the changes of the relative intensity of the main the emission peaks located at 540 and 580 nm, increased the ratio of I540/I580. The above results indicate that ZnO NPs have obvious negative effects on AE, which provides more information for a comprehensive evaluation of the bio-risks of ZnO NPs on aloe and other related plants.