Currently, nations grapple with a noticeable shortage of STEM talent, particularly within fields like agroforestry. The study applied the structural equation modelling and the mediation effect model to analyze the mechanisms through which STEM value perception influences STEM career preferences, as well as the roles played by STEM self-efficacy and STEM learning interest among 1,604 undergraduates majoring in agroforestry. The results revealed that students' STEM value perception was found to directly and positively correlate with their STEM career preferences. STEM value perception also has an indirect impact on STEM career preferences by influencing STEM learning interest and STEM self-efficacy. Furthermore, STEM value perception plays a sequential mediation role in promoting STEM learning interest, STEM self-efficacy and STEM career preferences. Based on these findings, it is recommended that institutions bolster STEM career education for students majoring in agroforestry from the outset of their enrollment, enhancing students' professional awareness and identity, by addressing gaps in students' value perceptions of STEM education. Furthermore, efforts to improve students' interest in relevant courses and their confidence in learning these subjects can be beneficial. Ultimately, such initiatives can contribute to a more balanced development of students' STEM career preference.