Facing the downward pressure of automobile industry, Chongqing’s automobile industry urgently needs to change development mode from high input and scale to high technology and high additional value. R&D input is the main factor to boost industrial innovative development, therefore, based on the research on the conduction mechanism of R&D input on industrial innovative development, this paper analyzes the correlation effect of R&D input of Chongqing’s automobile industry on its output, and finds that there is a positive correlation between the input of R&D funds and personnel and its patents and profit. The realization of industrial transformation and upgrading needs government to intensify the input, to overall integrate all kinds of funds, to optimize funds input structure, to build R&D talent team and to invest in kinetic energy for industrial innovative development.