With the rapid growth of science and research funding, research funds cost management is faced with more challenge. By comparing the cost management current situation of Chinese and the UK’s universities, we find out that disunity of costing approach, unreasonable design of indirect cost are the main problems of cost management of Chinese universities. Based on the comprehensive analysis of the UK’s full economic costing, suggestions on cost management mode, the costing system, the indirect costing approach are put forward against above problems.