Based on the international comparison, this paper found that basic research investment still exists the problem of insufficient funds and the structure to be optimized in our country. Investigating the reason, it can be explained from the existing policy and subjective understanding aspects. Analysis show that the current policies have various defects, such as giving prominence to application oriented, weakening the scientific orientation; highlighting R&D investment intensity, weakening basic research investment; standing out achievements transformation of colleges and universities, weakening basic research requirements. From the perspective of cognition, some misunderstanding, such as "useless theory of basic research", not worthwhile of basic research, low basic research investment being reasonable, has existed for a long time. This paper put forward some suggestions, that further discussion and study on the understanding of basic research, then reasonably determining the target of basic research investment intensity, and the central government funding of new R&D investment should mainly tilting to the basic research, and clearly position the R&D function of universities and colleges, etc.