Abstract:The problems arising from the management of scientific funds are chiefly found in the following aspects: incomplete system for scientific research management; greater focus on project making yet less focus on management; unscientific budget for the use of scientific funds; the inappropriate use of scientific funds; the irregular management of extra funds. The principal cause lies in a weak awareness for the management of scientific funds, flaws in the system for scientific fund management, a backward messaging system for the scientific fund management. Counter measures are suggested: management be reinforced through inner control; the ratio of labor cost fee and performance and results be properly increased; the activeness and enthusiasm of the scientific research staff be mobilized so as to prompt a healthy development of the scientific research in institutes of higher learning.