The invention provides a real-time clock error correction method used an exploration instrument. The method is a clock drift compensation method having a self-learning function. The method is used for compensating the influence of crystal oscillator frequency point drift on the system clock accuracy of the instrument. The method includes two functions of clock error learning and clock error correction. The clock error learning function provides the basis of clock frequency difference of the dynamic inspection work state. The clock error correction function monitors nodal ocean bottom seismograph clocks in work in real time so that the time accuracy of the nodal ocean bottom seismographs is ensured to be within a positive and negative sampling interval. The problem of difficulty of clock correction caused by great change of the common crystal oscillator frequency point along with external factors can be solved, and the method has the characteristics of being lightweight and easy to transplant.