In order to promote scientific inquiry in secondary schooling in Taiwan, the study developed a computer-based inquiry curriculum (including structured and guided inquiry units) and investigated how the curriculum influenced students' science learning. The curriculum was implemented in 5 junior secondary schools in the context of a weeklong summer science course with 117 students. We first used a multi-level assessment approach to evaluate the students' learning outcomes with the curriculum. Then, a path analysis approach was adopted for investigating at different assessment levels how the curriculum as a whole and how different types of inquiry units affected the students' development of conceptual understandings and inquiry abilities. The results showed that the curriculum was effective in enhancing the students' conceptual knowledge and inquiry abilities in the contexts of the six scientific topics. After the curriculum, they were able to construct interconnected scientific knowledge. The path diagrams suggested that, due to different instructional designs, the structured and guided inquiry units appeared to support the students' learning of the topics in different ways. More importantly, they demonstrated graphically how the learning of content knowledge and inquiry ability mutually influenced one another and were reciprocally developed in a computer-based inquiry learning environment.