The invention discloses a seabed comprehensive exploration system which comprises an exploration main body and a lotus root sinking frame detachably connected to the lower portion of the exploration main body. The exploration main body comprises a seabed base, a floating ball, a hydrophone, a seabed electric field instrument, a seabed magnetic field instrument, a seabed seismograph and an electrode arm; wherein the hydrophone, the seabed electric field instrument, the seabed magnetic field instrument, the seabed seismograph and the electrode arm are all arranged on the seabed base, and the electrode arm is in communication connection with the seabed electric field instrument. The system integrates main equipment required by current ocean exploration, is provided with an ocean bottom seismograph, an ocean bottom electric field instrument, an ocean bottom magnetic field instrument and a hydrophone, and can flexibly combine the equipment to match various different exploration tasks. The system is used for observation of seabed natural earthquakes, seabed MT and artificial magnetotelluric sounding, underwater acoustic signal recording, seismic tomography, earthquake activity and earthquake forecast and the like, and is comprehensive in function and good in applicability.