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Graduate education in Science and Engineering(S&E) plays an important role in nurturing talent for innovation-led growth in China. However, there is no consensus on whether market or government mechanism is more important in developing S&E graduate education. This study uses data from 2008 Beijing College Student Development Survey to examine the effects of market conditions and financial aids on graduate student’s intention to pursue S&E doctoral education. The study finds that knowledge spill-over effects and low skill impede human capital investment in S&E, while government financial aids promotes individual’s aspiration for S&E doctoral education. Compared with scholarship, assistantship is more effective to increase student’s doctoral aspiration.