Active inquiry plays a key role in science education. To facilitate children's motivation, alternate reality games are applied to engage children actively in inquiry in authentic learning contexts. However, the complexity of real-world contexts and the ambiguity of game puzzles increase the difficulty for children to conduct effective inquiries. To achieve successful inquiry-based learning, concept mapping is an effective learning strategy to guide children to organise related information as well as to brainstorm for possible solutions. Accordingly, this study proposes a mobile concept mapping-based questioning approach for environmental education. A quasi-experimental study was conducted to evaluate the effectiveness of the proposed approach and the conventional questioning approach in game-based inquiry-based learning. The results showed that the proposed approach had a more significant effect on learning achievement, critical thinking, and learning attitude than the conventional questioning approach. However, cognitive overload negatively affected the children's learning. Besides, it was found that improper use of concept maps could limit their creative problem-solving performances.