The invention discloses a method for obtaining the undercompaction overpressure in a stratum. The method comprises the steps that 1, firstly, according to the difference change characteristics of theaverage interval transit time, the average stratum density and the average neutron porosity of a mudstone section along with the average buried depth, the normal compaction section and the undercompaction section are determined; 2, then the index relation of the acoustic wave velocity and the vertical effective stress is fitted by utilizing a scatter diagram of the acoustic wave velocity and the vertical effective stress of the normal compaction section; 3, due to the fact that change of the vertical effective stress and the acoustic wave velocity of the undercompaction section needs to fall on a change trend curve of the acoustic wave velocity and the vertical effective stress of the normal compaction section, the acoustic wave velocity of the undercompaction section is substituted into the index relation obtained in the step 2, and the vertical effective stress of the undercompaction section is obtained; and 4, finally, the overpressure value in the undercompaction section is obtained by combining the relation of the vertical effective stress of the undercompaction section and the overpressure. The magnitude of the undercompaction overpressure can be accurately obtained only through logging data, the characteristics of rapidity, simpleness, convenience and accuracy are achieved, and the evaluation efficiency on the undercompaction overpressure is improved.