Depending on the innovation types, the main body of innovation and its optimal allocation of the capability and resource in the innovation process, the technology innovation mode by industry-university-institute cooperation can be divided into two types: one is the innovation mode through the enterprises that are established by the university; the other is the integrated innovation mode led by the enterprise. Under former mode, by using some tools such as theories and models including the dynamic games, principal-agent and real options et al., one dynamic games model is established from the systematic perspective containing the innovation capital acquirement, effective organization with the innovation process, market competition attending, and the sets with the sub-game perfect Nash equilibrium is also gotten under four different circumstances according to the newly enterprise as whether making finance and the organizing differences between different innovation process. Comparison analysis of different innovation process and the financing effects for the same ones were made under the fixed environment and dynamically uncertain ones, correspondingly, the differences and the suitable comparison condition between some parameters equilibrium outcomes containing the optimal innovation investment and bankruptcy threshold, R&D investment, risk, salary level, production and price with the innovation success and failure, expected profits, price and production were also concluded.