This manuscript outlines the Innovative Comprehensive Experimental Project (ICEP), which is highly interdisciplinary, practical, and relevant to current societal issues. The project serves as an excellent experimental teaching tool for graduate students of Chemistry, Pharmaceutical Engineering and other related majors. The experiment successfully combines the organic chemistry experimental techniques and bioactivity analysis skills learned by students during their undergraduate studies, which is vital for new graduate students to enhance their experimental proficiency. Through participating in hands-on training, students can not only effectively improve their ability to solve complex problems but also cultivate innovative thinking and scientific research competence in the process. The experiment begins with the pressing issue of bacterial drug resistance, prompting students to think critically about the relationship between bacterial resistance and the development of new antimicrobial drugs. This approach helps establish a proper method for using antimicrobial drugs. Throughout the experiment, students will synthesize 1,3,4-oxadiazole pleuromutilin molecules, evaluate their antimicrobial activity (in the Biosafety Level 2 laboratory), and simulate molecular docking. The interactive teaching method between teachers and students runs throughout the preparation, implementation, and summary parts of the project. This approach positively impacts students’ theoretical knowledge expansion, practical skill enhancement, and innovation ability cultivation.