Higher-order thinking is crucial to inquiry learning. It is important to investigate how students think in inquiry contexts. Given the tacit nature of higher-order thinking, cognitive maps (e.g., concept maps, reasoning maps) have been used to externalize thinking and have shown promising effects in terms of improving inquiry task performance. However, few studies have analyzed student-constructed maps that reflect the thinking underpinning students' inquiry task performance. This study aimed to address this gap. Sixty-nine 11th grade students worked in small groups to explain a fish die-off phenomenon in a virtual ecosystem and collaboratively constructed an integrative cognitive map to facilitate thinking during the task. The map comprised a concept map (representing conceptual thinking about relevant subject knowledge) and a reasoning map (representing the reasoning process). Regression analyses showed that the quality of the student-constructed maps, particularly the reasoning maps, was a significant predictor of inquiry task performance assessed based on students' written explanations of the phenomenon. Although the quality of the concept maps was not a significant predictor of inquiry task performance, it did predict the quality of the reasoning maps. Student thinking reflected in concept mapping and that reflected in reasoning mapping play different roles in inquiry learning.