Engineering design thinking is at the core of engineering competence. Project-Based learning (PjBL) about Science, Technology, Engineering, and Mathematics (STEM), which is based on engineering design, has brought enormous success in students' gaining and applying knowledge about STEM subjects. However, there are few studies on the perceived improvement in engineering design thinking and the possible role that learning style (LS) plays. We implemented PjBL-STEM classes to enable students to design and build a water tower using a truss tower structure that can withstand earthquakes. Constraints such as height, load weight, tower weight, and degree of earthquake withstanding were included. A total of 137 Taiwanese students participated in this course and employed a Gregorc learning style delineator to determine their learning preferences. A pre-test and post-test on perceived engineering design thinking performance was also undertaken. Students demonstrated significant improvements in their perceived engineering design thinking. Additionally, abstract-type learners had greater perceived improvement than concrete-type learners from the PjBL-STEM course. We suggest that different pedagogical methods should be utilized to provide equal opportunities for each student.