The engagement in research, as the primary form of learning engagement for PhD students, is crucial for enhancing their competitive edge. Academic passion, a key determinant of learning engagement, plays a significant role in driving the research enthusiasm of PhD students. However, the "black box" concerning whether and how academic passion influences PhD students’ research engagement remains to be explored. Addressing this gap, the present study draws upon self-determination theory, adopts the "motivation-behavior-effect" analytical framework, and incorporates ambidextrous learning as a mediator to elucidate the specific pathway through which academic passion impacts PhD students’ engagement in research activities. Furthermore, it examines the facilitating role of the academic climate in this process. From December 2022 to March 2023, a questionnaire survey was conducted, collecting 522 responses from PhD students across 25 universities in China. The survey primarily assessed the PhD students’ academic passion, ambidextrous learning behaviors (including tendencies towards exploratory and exploitative learning), and their perceived academic climate, investigating how these factors collectively influence their engagement in research activities. The questionnaire data were analyzed using a combination of SEM and bootstrapping with SPSS 26.0 and Mplus 8.3 software. The findings reveal that academic passion significantly positively affects PhD students’ research engagement; ambidextrous learning (exploratory and exploitative learning) mediates the relationship between academic passion and PhD students’ research engagement; and the academic climate effectively facilitates the transformation of PhD students’ academic passion into ambidextrous learning (exploratory and exploitative learning). The study’s conclusions not only foster PhD students’ enthusiasm for research but also enhance learning effectiveness and innovation vitality, providing a theoretical basis for reforming the doctoral training system.