The invention relates to an automatic correction method and system of a padding height measuring machine. The automatic correction method comprises the steps that S1 a carrying hole is formed in a machine platform or an outer frame of the padding height measuring machine, and a correction sampler wafer is installed in the carrying hole; S2 the correction sample wafer is shot through a probe of the padding height measuring machine, and a standard image is selected; S3 the current of the probe is adjusted so that the brightness and the grey scale of the image shot by the probe can be matched with those of a standard image. Through the automatic correction method and system of the padding height measuring machine, a detection light source of the padding height measuring machine is corrected, the brightness of the light source is made to be more stable, and therefore the measuring accuracy of the padding height measuring machine and the stability of the detection result are guaranteed. In addition, the service life of the detection light source can be prolonged by adjusting the current.