The invention discloses a floating roll-in benthic type submersible control system which is characterized by including a water surface planning platform and an underwater control platform which can bein wireless communication with the water surface planning platform; the water surface planning platform comprises a main control module, a task planning module, a global path planning module and a global database module; wherein the underwater control platform comprises a local path planning module, an action behavior set module, a local database, a path planning mode switching event detection module, a path planning mode switching event identification module, a re-planning trigger module and a real-time local environment sensing module. The control system has the beneficial effects that therequirements of the operation tasks under the seabed complex terrain environment can be met.