Seafloor observatories enable long-term, continuous, real-time, weather-independent, and multidisciplinary scientific observation and research that will promise major breakthroughs in ocean sciences. China has started to establish a seafloor observation system in the East China Sea (ECSSOS), and the purpose of this paper is to describe the remote control for ECSSOS. Technological development in system architecture and remote communication was first performed in this paper. Based on this work, an overall framework for the remote control solution for ECSSOS was developed, adopting a client-server architecture containing three components, that is, a control center, a shore station, and observatory facilities, as well as two strands of information flow, that is, flow of observation data and flow of control commands. To implement the present solution, operational data flow and the core module were further designed and the corresponding remote control subsystem for ECSSOS was developed against all design specifications. This backbone system has been put into operation in China's first seafloor observatory in 2009, and in this paper the practical performance is evaluated addressing both the general descriptions and results from case studies. Given the successful trial in the Xiaoqushan seafloor observatory, the remote control solution proposed in this paper could be a useful reference implementation to the following construction phases of ECSSOS.