Intergovernmental science and technology cooperation (ISTC) means in order to implement the science and technology policies efficiently, the central and local governments form a mutual interacted cooperation system. Generally speaking, the governments often establish the stable bilateral or multilateral cooperation relationship by signing the intergovernmental contracts, founding unite organizations, convening joint conferences and so on. There are theory and practice backgrounds for this emergence. This kind of cooperation has benefited a lot to promote our science and technology management system reform, optimize the science and technology resource distribution, and establish the national and regional innovation system.