The intellectualized detection technology is important in the seafloor magnetotelluric acquisition. The key problems encountered during the signal acquisition are large quantities of detection information, long working time on the seafloor, serious disturbance of the environment and complex logical control. These problems could not be solved without intellectualized measures. In fact the procedure of intellectualizing the seafloor magnetotelluric acquisition is the procedure of applying the computer technology to the acquisition autocontrol, automatically saving the data with the circuit having immunity. Considering the specific characteristics of the operation in the ocean engineering, the PC104 is inset in the seafloor magnetotelluric instrument as a control unit. Several control interfaces are selected and the controlled positions are arranged correctly. The circuit driver takes into account the compatibility of various interfaces. The instrument has been proved to be effective and practicable through the marine experiments.