Private enterprises are major contributors to China's market economy. In order to ensure the sustainability of economic development, China pays more attention to the role of science and technology in promoting the sustainability of the private economy. Based on a sample of all A-share listed companies in the Chinese capital market, we distinguished between government and non-government purchase order data, and examined the impact of large government background customers on private enterprise R&D innovation from the perspective of supply chain risk transmission. Due to the implementation of China's new accounting standards and the delay in the public update of government procurement data, we selected samples from 2007-2015. The research results show that the government background customers can significantly increase the R&D investment of private enterprises, and this relationship is more significant in the sample of mid-level government background customers and private enterprises in poor areas; further analysis found that government background purchase orders can promote innovation investment by mitigating the risks facing a company. From a practical point of view, the research findings of this paper are helpful for understanding the impact of customer structure on the innovation activities of enterprises in a market economy environment.