Against the backdrop of globalization and multicultural integration in Southeast Asia, PhD education is transforming from traditional mentorship to online collaborative learning. This study examines four Malaysian universities through surveys of 80 PhD students and 20 supervisors, exploring the application, complementarity, and challenges of both models. Results show online collaborative learning significantly enhances research output and international participation, while traditional mentorship remains irreplaceable for personalized guidance. The hybrid integration of both models is optimal for high-quality PhD education in Southeast Asia’s multicultural context.