In this study, we have developed a novel teaching aids for learning fundamental stereoisomerism in organic chemistry (OC) through modern techniques of augmented reality (AR). The instructional module is based on a problem-leading learning in class activity through the assistance of our virtual tools. The lesson plan was divided into three subjects including structural representations/interconversion for organic molecules, conformation/configuration isomers, and enantiomers/diastereomers. Moreover, the organic reactions involving specific stereochemistry concepts and the correlations for their isomeric products can be also conducted in the class activity using our AR tools. Comparing with in-class training by physical model kits, students can perform self-training/instruction at home through the assistance of AR teaching aids. Students themselves also agree that the virtual tools did help to understand complex stereoisomerism in OC. The AR teaching aids were now available on Google Play and the App Store.