Based on the panel data of national agricultural research institutes in China from 2013 to 2020, the Stochastic Frontier Analysis is used to analyze the influence?of different types of research funds on the efficiency of basic research and achievement transformation of research institutes for the first time under the premise of controlling the regional differences and institutional characteristics of research institutes. And the heterogeneous impact of the two types of funds on high-quality basic research is also considered. It is found that the increase of block funding can significantly improve the efficiency of basic research and achievement transformation, but have no significant effect on the efficiency of high-quality basic research. There is an inverted U-shaped relationship between competitive funding and the efficiency of basic research, and the funding has a significant positive correlation with the efficiency of achievement transformation. At the same time, there is also a significant positive correlation between it and the efficiency of high-quality basic research.