The core of industrial upgrading and industrial chain modernization is the technological innovation of the enterprises. Only by the collaborative innovation of the upstream and downstream enterprises, the industrial upgrading and industrial chain modernization can be realized. Therefore, it is of practical significance to study the collaborative innovation of the upstream and downstream enterprises. By establishing an industrial chain model of an upstream enterprise and a downstream enterprise, this paper analyzes four cases of collaborative innovation. Using ‘Matlab’ to analyze the profits of the upstream and downstream enterprises and the industrial chain in four cases with the change of the innovation risks, it is found that within a certain range of innovation risks, collaborative innovation can bring out more profits for the upstream and downstream enterprise and the industrial chain, also the innovation effect of the upstream enterprises is higher than that of downstream enterprises. Therefore, the government should actively support the technological innovation of the raw material suppliers that in the upstream chain, so as to realize essential technical breakthroughs and industrial chain modernization.