Since the 1990s, higher education in the developing countries has gone through great changes in response to their fundamental political and socio-economic reforms. China and Malaysia, the two main Asian developing countries with emerging economies and ambitious goals, were picked up for a comparison of higher education development to better illustrate this general trend. In this comparative framework, comparability about the two countries is analyzed firstly, followed by the consideration of three key dimensions, and George Bereday's method of comparison is accordingly used. It is noted from the comparison that both Chinese and Malaysian higher education systems have experienced massification, marketization and internationalization, and are currently striding toward universalization with more excellence-driven initiatives of higher education, which involve the main mechanisms and rules, as well as strategies and policies of marketization and internationalization. Yet other than the commonalities at a macro level, in these three areas concerning higher education there are some remarkable differences and disparities, such as the actual paths of size expansion, the growth and fate of private institutions, the conception of internationalization, due to different historical paths, national agendas and socio-political environments. Along this comparative approach, there are three common issues that need further elaborate discussions, namely, the unbalanced structure of quantitative development, centralized decentralization, and internationalization at home.