In order to enable urban economic development, the use of the right value and asset value of rural collective construction land (RCCL) is increasingly becoming apparent and this market is experiencing rapid development. However, the arrangement of the governance structure of rural shareholding cooperatives (RSCs) can seriously affect the efficiency of collective construction land market transactions, since the governance of RSCs is related to the interests of farmers. Protecting the rights and interests of farmers while improving the governance efficiency of RSCs is a considerable challenge worldwide. To better deal with this challenge, this study used a field survey in Nanhai District, Guangdong Province, China, to estimate how the governance structure of RSCs affect the efficiency of RCCL market transactions. Tobit models were constructed, and the results show that (1) most of the governance functions of RSCs were not separate from the administrative management of the village committees, which leads to low efficiency of RSCs’ governance; (2) leaders of rural collective economic organizations played a key role in governance efficiency; (3) from the perspective of collective land property rights, most village shareholders did not have decision-making power or supervisory authority in the RCCL transfers because they could not complete access to transaction information. Furthermore, most villagers felt that the amount of income distributed was unreasonable, and the rights and interests of farmers and village shareholders were not guaranteed by the RSCs. Therefore, we suggest that the Chinese authorities should strengthen their current efforts to construct a more open and fair governance structure of the RSCs and thus improve their market transaction efficiency. Our work provides some insights into ways to improve the governance structure and market transaction efficiency of RSCs, which can further contribute to the development of the RCCL market in other areas of China and worldwide.