The quality of classroom education is essential to the construction and development of departments and colleges, and a mirror of the teaching level and quality of teachers. Project-based learning (PBL) tries to create problem scenarios for learners, and encourage them to think deeper and communicate more. Inspired by PBL, this paper analyzes the existing evaluation index systems (EISs) for classroom music education in colleges, and summarizes the application of PBL in music teaching. Besides, a novel EIS is designed and constructed for classroom music education. The results show that: PBL stresses the changes of learners through the learning, and enables teachers to combine pre-, in-, and post-class methods to comprehensively evaluate the music literacy of students; PBL exerts a positive effect on students’ learning. The results lay a theoretical basis for reforming the EIS of classroom music education.