PurposeThe purpose of this paper is to investigate the influence of organizational structure (OS) of innovation teams and the external support mechanism on the commercialization of a small‐ and medium‐sized new venture.Design/methodology/approachTaking the perspective of inter‐organizational cooperation, this paper tries to adopt complementary view of transaction cost economics and resource dependency theory and employ enterprises in incubation centers in Taiwan as the empirical subjects. More specifically, this paper analyzes how organization structure (formalization, decentralization, specialization, and socialization) and the support mechanism (technology support, management training, administrative support, and commercial support) affect commercialization as well as the interactive effectiveness of organization structure and support mechanism for new ventures in incubation centers.FindingsBased on the results of the empirical investigation of enterprises in incubation centers, three conclusions are drawn. It is apparent that organization structure influences efficiency and competence building. Second, support mechanism has a positive effect on commercialization. Third, if considered the cross effect of OS and support mechanism, it shows positive effect on efficiency but not on competence building; and tech‐support has its positive effect to improve competence building.Originality/valueThis paper identifies the importance of arrangement of governance mechanisms including organization structure of innovation team, external support mechanism, and their cross effect on commercialization of small and medium enterprises.