The present invention relates to a system and a method for selecting a research and development project through autonomous proposals of evaluation indicators, in which performance information generated according to a selection of performance evaluation items for research and development project bidding is classified by bidders, and the research and development project is selected for each classified bidder group. The present invention allows research and development project bidders to select evaluation indicators which serve as criteria for selecting a research and development project, thereby being capable of guaranteeing autonomy and providing fair bidding opportunities to all research and development project bidders. Also, since a research and development project is selected for each group classified according to the autonomously selected performance evaluation items, transparent selection and fair competition between the research and development project bidders can be ensured, and research and development projects can be equally divided.