The invention discloses an in-situ measurement system and method for spatial distribution of spin polarizability of an alkali metal atom magnetometer, and belongs to the technical field of precision measurement. The system is mainly composed of a laser, a laser stabilizing system, a laser beam expanding system, a beam splitting prism, a polarization element, a magnetic shielding system, an alkali metal atom gas chamber, a photoelastic modulator, a photoelectric detector, a CMOS sensor, a data collecting, analyzing and processing system and the like. The system has reasonable theoretical basis and simple experimental operation, no additional system disturbance is brought to normal operation of the magnetic measurement system, the electron polarizability distribution of the working state of the alkali metal atom gas chamber can be accurately measured, the measurement sensitivity of the atom magnetometer can be improved on the basis of the polarizability distribution measurement result, and a basis is provided for development of an ultra-high-sensitivity extremely-weak magnetic measurement device.