Southeast Asian Studies is a new secondary discipline of International and Regional Studies，which can provide intellectual support for building a closer China-ASEAN community of shared future. Therefore，it is particularly necessary to strengthen the discipline construction of Southeast Asian Studies. Research methods are the basis of Southeast Asian Studies，and strengthening the construction of research methods is the key to improve Southeast Asian Studies. Therefore，scholars of Southeast Asian Studies need to pay close attention to and conduct in-depth research on research methods. This paper takes the internationally authoritative SSCI journal as the research object，namely，the Journal of Southeast Asian Studies，and makes an in-depth analysis of the research methods used in the papers published by the journal in the 23 years after the 21st century，including case study method，comparative research methods，historical research method，literature research methods，fieldwork method，interview methods，questionnaire methods，and mixed research methods，which comprehensively presents the current situation of the use of research methods of Southeast Asian Studies. Through the study of the Journal of Southeast Asian Studies，this paper summarizes the beneficial implications of the construction of research methods of Southeast Asian Studies. Specifically，Southeast Asian Studies needs to adhere to the overall pattern of diversified research methods，attach importance to the combination of theory and empirical research methods，strengthen the mixture of qualitative and quantitative research methods，and reflect the value of case studies and comparative studies，so as to form a scientific system of research methods of Southeast Asian Studies.