Abstract:The low allocation efficiency of independent R&D investment in China is one of the important reason for the low independent innovation ability and innovation performance.From the perspective of internal and external expenditure on independent R&D, this paper brings the knowledge stock into the analysis framework, and constructs a threshold model using the data of 28 provinces and cities in China from 2009 to 2017. The study finds that there is a significant knowledge stock threshold effect in internal and external expenditure on R&D, and low knowledge stock areas contribute more to the marginal output of innovation performance than high knowledge stock areas. The sub regional analysis shows that in the external expenditure model with knowledge stock as the threshold, the western region is different from other regions, and its high knowledge stock regions contribute more to the marginal output of innovation performance. The research of this paper provides a basis for the innovation subject to reasonably allocate R&D investment, especially government intervention.