The use of external representations has the potential to facilitate inquiry learning, especially hypothesis generation and reasoning, which typically present difficulties for students. This study describes a novel three-dimensional cognitive mapping (3DCM) approach that supports inquiry learning by allowing learners to combine the information on a problem, the subject knowledge, and the hypothesizing and reasoning process involved in the exploration in a single image. The study also investigates the influences of the 3DCM approach on knowledge achievement and learner perceptions within an online inquiry-learning context. Forty-eight 11th-grade students used 3DCM to complete an inquiry task. Data were collected from multiple sources, including pre- and post-tests, questionnaires, and semi-structured interviews. The results revealed that the students showed high levels of academic achievement, positive attitudes toward inquiry learning, low levels of anxiety, and medium levels of confidence. A post-hoc test indicated that the students at a low academic level had acquired significantly more knowledge than either the high-level or medium-level students, thus narrowing the academic gap between low-level, medium-level, and high-level students. In addition, the participants' attitudes and degree of confidence were found to be positively related to their inquiry skills, such as hypothesis generation and reasoning. The implications of the study and directions for future work are also discussed.