Within the last decade, Thailand has emerged as an innovation achiever, partly due to its aggressive interest in developing its national innovation system by increasing its research and development (R&D) investment. However, evaluation of the productivity of such policies has been found to be unfit for the conditions of this emerging ecosystem. This study proposes a systematic method to examine which collaboration factors affect Thai firms' R&D productivity and how these reflect on industry sectors' dynamics. The model is tested empirically through a dataset of 44 industry sectors collected directly from the National Innovation Status Survey from 2011 to 2016. The results explore the number of inventions, patent applications and granted patents as factors that influence collaboration between firms within the university and the public sector. The tailored analytical model may be useful in future efforts to assess R&D collaboration amongst industry and government sector stakeholders in other developing countries.