Abstract: This study established an input-output model for institutionalized scientific and technological innovation, to characterize innovative knowledge output of world-class research disciplines. Rising above traditional evaluation indicators like papers and patents, prizes with strong recognition among global academic communities, generous financial bonus and great honor can be used to compare the innovation prowess of countries and institutes within and across disciplines. Thus, this study built an evaluation system of well-defined Prize Reputation Index, National Differential Index, Advantage Attenuation Index, and the synthesis of Index of Discipline Advantages to map out the value of such award recognition. Based on 6469 winners of 176 world famous prizes from 1981 to 2020, this study analyzed 261 research institutes and 480 universities from 71 countries. The results show that, although China as a country ranks 12th in general, and that Tongji University and China National Hybrid Rice Research and Development Center made it into the global top 10 of architecture and agricultural disciplines respectively, recognition in the form of awards and honors to Chinese recipients lags far behind the share of publications by Chinese scholars in international journals. Such a difference reveals the gap in major original innovative knowledge output between China and the developed world, which should warn us not to evaluate discipline development, draft development strategies, or allocate R&D resources solely with “good-looking” international publications and other publication-based indicators, lest it causes severe strategic misjudgment. Based on existing drawbacks in China’s current R&D organization and relevant performance evaluation model, the paper also provides the following suggestions for future policy-making: a, set up the necessary criteria to appraise the recognition of Chinese R&D efforts by renowned international awards and, in turn, include it into S&T statistics and evaluation system; b, change the evaluation approach that links the merit pay of researchers directly to their annual appraisal results; and c, China’s S&T award system should improve its identification of original innovation, broaden global vision, and set up its own international S&T awards with Chinese characteristics.