Professional certification is an important way to promote professional construction and the quality of personnel training. Undergraduate thesis is an important part of comprehensive training for agricultural students, and it is also one of the "prescribed actions" of professional certification examination. Based on the perspective of professional certification, taking the graduation thesis of Agronomy Major of Southwest University in recent five years as an example, this paper analyzes the reasons for the gap between the quality of graduation thesis and professional certification standards, and puts forward six paths to improve the quality of graduation thesis of agricultural undergraduates, such as more independent topic selection, more diversified forms, multilink submission materials online, relaxed time, and adding graduation thesis index We should guide the project, link up the construction of professional core courses, build a "learning community between teachers and students".