The purpose of this study is to understand the learning outcomes of students who participate in interdisciplinary hands-on advanced technology courses and the factors influencing their outcomes as well as to determine whether learning outcomes and cognitive development are affected by students’ motivation for selecting the course with regard to their learning abilities. The subjects of this study are students who were enrolled in interdisciplinary advanced technology courses at a university located in Northern Taiwan from 2020 to 2021. We recruited 171 students to complete measures of their motivation for selecting the course and to complete a prelearning outcome scale during the first week; a learning abilities scale was completed during the ninth week; and a postlearning outcomes scale was completed during the sixteenth week. We recruited 96 students to participate in interviews after they completed the course to determine their cognitive development. The results showed that participants’ average learning outcomes scores on the posttest were significantly higher than those on the pretest. After students participated in the course, 66.7% of them were in the “Apply” stage, indicating they could apply the knowledge they learned to other situations, while 25% were in the “Analyze” stage, indicating they could deconstruct the course knowledge based on its structure and understand the correlations among various items of course knowledge. Participants’ interdisciplinary abilities were found to mediate the relationship between their autonomous motivation and cognitive development.