Learning physics is challenging at all levels. Students' difficulties in the introductory level physics courses have been widely studied and many instructional strategies have been developed to help students learn introductory physics. However, research shows that there is a large diversity in students' preparation and skills in the upper-level physics courses and it is necessary to provide scaffolding support to help students learn advanced physics. This thesis explores issues related to students' common difficulties in learning upper-level undergraduate quantum mechanics and how these difficulties can be reduced by research-based learning tutorials and peer instruction tools. We investigated students' difficulties in learning quantum mechanics by administering written tests and surveys to many classes and conducting individual interviews with a subset of students. Based on these investigations, we developed Quantum Interactive Learning Tutorials (QuILTs) and peer instruction tools to help students build a hierarchical knowledge structure of quantum mechanics through a guided approach. Preliminary assessments indicate that students' understanding of quantum mechanics is improved after using the research-based learning tools in the junior-senior level quantum mechanics courses. We also designed a standardized conceptual survey that can help instructors better probe students' understanding of quantum mechanics concepts in one spatial dimension. The validity and reliability of this quantum mechanics survey is discussed.