Project system is an important resource allocation mechanism with some typical features including competitiveness,tech- nicalization and campaign - style. Since overflowing financial system and entering higher education field,Project System plays a much more important role and improves the development of higher education powerfully. The operational logic of Project System in higher ed- ucation takes the matter - doctrine logic,competitive and preferential logic and regulating and controlling logic as the logic beginning, the logic means and the logic target respectively. As a type of tool and means,however,its limitation brings out lots of unexpected neg- ative outcomes. From the state,inter - school and inner - school perspectives,it mainly includes the dispelling of the country's pur- pose,the inter - school homogeneous imbalance and inner - school academic ecological alienation.