Both Cathay Biotech and Genomatica in the United States utilize synthetic biology routes to produce long-chain dicarboxylic acids, sharing similar technological approaches. However, the two companies differ in their accounting treatment of R&D expenditures regarding capitalization and in the assessment mechanisms for government subsidies. These differences have, to a certain extent, led the two enterprises to choose distinct R&D models. From the perspective of innovation performance, Cathay Biotech’s autonomous vertical integration innovation model outperforms Genomatica’s open collaboration innovation model in terms of shortening the trial-and-error cycle and improving product gross profit margins.