Industrial enterprises are the main body of national scientific and technological innovation activities, and the improvement of their research and development (R&D) output capacity plays a pivotal role in the enhancement of national innovation capabilities. The R&D process is an input–output process, and its results have various forms. In this study, we construct a multi-objective R&D investment allocation optimization model from three dimensions representing China’s innovation capability, and propose a novel multi-objective mutation flower pollination algorithm (MOMFPA) to solve the model. We employ a two paired-sample T-tests to test the difference hypothesis of the model, and the test results show that the model is effective and reasonable. The MOMFPA and the weighting algorithm are respectively used for empirical analysis, and the optimized results obtained by the MOMFPA are found to be better than those obtained by the weighting algorithm, thereby demonstrating the validity and application value of the MOMFPA. Moreover, the multi-objective model is used to predictively optimize China’s future R&D investment. The forecasting results indicate that China should focus on increasing the proportions of R&D investment in high-tech equipment manufacturing and electronic information technology, while reducing the proportions of R&D investment in traditional industries, such as mining, food, paper, and metallurgy.