The invention discloses a comprehensive control method and device for achieving offshore geophysical exploration. The method includes the steps that the comprehensive control device obtains GPS time information, GPS position information and sensor information periodically; the comprehensive control device judges the effectiveness of the GPS time information according to the obtained GPS time information and a preset deviation threshold value and performs reference interval updating and chronometer time calibration; the comprehensive control device marks obtaining moments of all information in first comprehensive information and second comprehensive information according to the obtained GPS position information, the sensor information and the chronometer time and sends the marked first comprehensive information and the marked second comprehensive information to a navigation working station; the comprehensive control device obtains gun control starting information and extracts and sends a shooting instruction to a gun control system; gun control synchronous information is obtained, and record information is sent to a comprehensive recording system. According to the technical scheme, due to the judgment of time effectiveness based on a reference interval, it is well avoided that ineffective time is used for time calibration, and therefore the requirement for high-precision and high-reliability comprehensive control is met.