Family firms tend to be independent or collaborative in their R&D decision preference. What preferences are presented in the selection of partners? This is an important theoretical issue in the research of innovation strategy. Based on resource-dependent theory and social emotional wealth theory, this paper analyzes the influence of family control on R&D decision preference and the selection of partners, and discusses the boundary conditions between them using a forward-looking feedback model. Based on data from Chinese pharmaceutical listed companies, this study finds that, family firms are more inclined to choose a collaborative mode than non-family firms. In order to maintain social emotional wealth, they tend to avoid cooperation with state-owned institutions and prefer to cooperate with related enterprises. Heterogeneity analysis indicates that the R&D decision preference of family firms are also influenced by the level of social trust and property rights protection. The performance expectations plays a significant regulatory role in the R&D decision preference regarding family control and invention patents. That is, the performance expectation inhibits the willingness of family firms to collaborative in R&D, especially with state-owned institutions, but significantly increases their motivation to cooperate with related enterprises. This study provides new insights into the R&D decision preference of family firms.