Management control systems (MCS) are fundamental to the progress of research and development (R&D) activities. However, misunderstanding the functions of MCS impedes their scientific design. In view of this, we assess the literature on the key mechanisms of MCS in an R&D context according to the contingency and resource-based theories, and propose a framework which effectively demonstrates these mechanisms. The framework divides the progress of R&D into three stages and analyses the effects of control mechanisms on different R&D activities by distinguishing between their different functions. Finally, we verify the rationality of our framework, with a view to improving current MCS design, using a field study. Our work can help organisations to recognise the role of MCS and provides valuable theoretical and empirical evidence to support their R&D activities.