With R&D funding allocation of resources in the colleges and universities of 31 provinces and regions, this study make a qualitative analysis from four aspects:R&D funding scale, intensity, the structure of the source and the expenditure structure. The result shows that there is a big difference between the R&D funds distribution, investment and spending of 31 provinces and regions. On the whole, the R&D expenditure is insufficient and intensity is low; uneven distribution of the eastern and western universities; funds mainly come from the government; and the proportion of expenditure in basic research is too low. In view of the above problems, the study will propose countermeasures and suggestions from the government, universities and foreign advanced experience.