Purpose: The purpose of this study was to develop the augmented reality (AR) educational program combined with the instructional guidance for supportive learning, which enhanced the thinking process cooperative discussion and problem-solving skills in chemistry subject. Design/methodology/approach: The method used the quasi-experimental research design. Of the 45 students who attended this experiment, only 25 with low achievement qualified in operating the AR learning system of saponification and transesterification environment (ARLS-STE) system. Findings: These results confirmed that the AR educational program could have increased substantial benefits in improvements of students' knowledge and the ability of the thinking process for the participants with the lowest score. In semi-structured interviews, most of participants enjoyed manipulating the ARLS-STE system, which was realistic, motived and interesting for learning science subjects. Originality/value: The low-achieving students have often been known with a low learning capability, and they lack in developing constructional knowledge, despite being keen for learning. Regarding educational concerns for this population, providing orientated learning and supportive materials could increase their learning effects. Virtual worlds are an efficient learning tool in educational setting. The AR can offer visual concepts and physical interaction for students with low achievement in learning. Thus, this study investigates the acceptability of an educational program designed in the ARLS-STE, which involves the learning effects of academic knowledge and the capability of thinking process for students with low achievement. The ARLS-STE system was developed for this proposal, based upon the marker-based AR technologies combined with hands-on manipulation.