In summary, two PBL projects were elaborately designed to enable students practicing first principles thinking to promote both learning of fundamental principles in chemistry and using the fundamental principles to generate solutions for research problems. PBL project 1 was focused on constructing kinetic models based on chemically fueled assemblies. To strengthen the practice of first principles thinking for students through working on the project, cascades of coupled inquiries (inquiry-based technique) were designed and used to drive the students to reversely breakdown the problems to the foundations in 235 physical and organic chemistry through regular supervision meetings. The learning of the foundations was strengthened and kinetic models were sucessfully built. PBL project 2 was focused on synthesizing a target compound. In this project, Jigsaw method was used to allow students to learn the fundamental principles in organic chemistry and apply the foundations to product synthetic routes. Through applying first principles thinking, the learning depth has been increased. We have also seen the sign of 'creativity'