Student-centered teaching has become increasingly common in higher education as researchers have demonstrated its efficacy in recent decades. Herein, we hope to establish an efficient problem-based learning (PBL) method, which can help upper-division students learn organic chemistry content by combining teaching materials, experimental literature, and computational methods in a self-directed way, systematically and deeply. We aim to cultivate the critical-thinking skills of students and to expand modern research methods to analyze, predict, and understand organic chemical processes. On the basis of such goals and ideas, we take the practical Friedel-Crafts alkylation reaction as a model reaction. We focus on two key points, the pre-equilibrium and the rate-determining step (RDS). In combination with the textbook knowledge and DFT calculation method, we attempt to promote the upper-division students to further discuss and understand reaction details, including kinetic-controlled reactions, the Hammond-Leffler postulate, and the Curtin-Hammett principle, etc. Following this approach, we achieve our goals to discuss the Friedel-Crafts alkylation reaction and provide juniors with a deep understanding of the carbon-carbon bond formation reaction. Furthermore, students initially master the DFT calculation method and make a direct connection between experimental observations and computational results. This approach activates students' study interests to further use core ideas of structures and bonding to rationalize complex chemical reaction phenomena for their future learning career.