This paper introduces the design and implementation of the control subsystem. The control subsystem can be divided into monitoring data collection platform underwater and communication platform on water which respectively realize collecting and storing monitoring data of vertical profiler and satellite communi- cation. Water platform and underwater platform use AT91SAM9260 as core chip which has abundant port resources, to satisfy various profiler of the data collection, storage and communication needs. Experiments show that the control subsystem functions perfectly, operates stably, which meets the design requirements.