As an important approach to learning and teaching, project-based learning (PBL) addressed in new curriculum reform at the middle school level in China raises the need for change in teachers’ beliefs, since teachers’ beliefs are important factors that influence their acceptance, adaptation, and implementation of PBL. Using qualitative content analysis, this study examined 23 prospective teachers’ (PTs) perceived beliefs shifts through participating in a systematic PBL program at a university. Data were collected from two open questionnaires for pre- and post-tests, respectively, which were about the beliefs about the nature of mathematics (BNM), beliefs about learning mathematics (BLM), and beliefs about teaching mathematics (BTM). The results revealed that PTs’ beliefs about BNM, BLM, and BTM were significantly shifted from the instrumentalist view or the Platonist view to the problem-solving view and that their shifts in BNM positively influenced the shifts in BLM and BTM. The implication for teachers’ professional development is that transforming teachers’ beliefs through systematic training on the theory and practice of PBL is feasible before implementing pedagogical innovations featuring PBL on a large scale.