The world is faced with dual challenges to ensure food security for its large and still growing population and to mitigate climate change. It is necessary to develop more diversified and multifunction agricultural systems to address the challenges. Therefore, as a reasonable land use practice, agroforestry has become the hotspot in scientific research in recent decades. This study performed quantitative and qualitative analyses of agroforestry research published between 1990 and 2018 based on bibliometric methods, expecting to guidance for further research in order to scientifically understand of the trends and features of agroforestry research over time and by region. A total of 4204 publications were obtained from Web of Science. The results show that the research interest in the agroforestry field has significantly enhanced, and about 139 countries have been involved with the research in this field. These publications cover 66 subject categories and a great diversity research theme. Since 1990, the popular keywords in agroforestry research have been changed from “Intercropping”, “Alley cropping”, and “Multipurpose trees” to “Carbon sequestration”, “Ecosystem service”, and “Climate change”. This indicates that the theme of agroforestry research has changed and the research scale is gradually expanding. Furthermore, agroforestry research themes vary with regions, since different regions have various requirements on the function of the agroforestry system. In the end, given the current trend of agroforestry science, we conclude a list of research potentials of agroforestry in the future.