Informal science learning has drawn the attention of researchers, educators and museum administrators for a long time. However, the problem of how to better support visitors to be more engaged while visiting exhibits and improve informal science learning performance is still missing. Context-aware technologies have the advantages of fostering learning interest and providing real time feedback. Previous studies have examined the effectiveness of 5E Learning Cycle in science learning. To address the problem, this study aims to develop a mobile label assisted system using the 5E Learning Cycle approach based on iBeacon technology in a science museum. A total of 43 college students participated in this study. Participants from different majors were assigned to two groups in an effort to make the groups relatively equivalent in terms of student majors. One group was the experimental group (mobile label assisted visiting mode, n = 21), and the other one was the control group (traditional visiting mode, n = 22). From the results of learning performance, stay-time, behavioral pattern analysis, and interviews, it was found that the mobile label assisted system can effectively guide visitors to interact with exhibits, conduct thoughtful learning, and prolong the visiting stay-time. Visitors are willing to visit the science museum with it. This was one of the very few studies focusing on the application of iBeacon to design mobile label system in a science museum. It turned out that iBeacon technology has huge potential applications for the future science museum.