Aiming at solving the problem that mechanisms act ineffectively in our science and technology cooperation project (STCP) management and combined with the STCP development trend, this paper discusses the necessity to improve the management mechanisms, and pointes out the drawbacks of the present STCP, i.e., the related rules of law and the supervision and the evaluation mechanisms are incomplete. It puts forward the countermeasures to implement scientific management of STCP and improve the management efficiency from the perspective of overall STCP procedures.