The invention discloses a full-automatic scanning system and a method for a microscopic section. The system comprises an object stage, a lighting device, an object lens, a Z-axis controller, a scanning camera and a computing device, the scanning camera is provided with a rolling shutter exposure mode and a banded array or banded subarray reading mode, the scanning camera performs a continuous digital imaging scanning for a banded partial area of a section sample which moves at a constant speed along a shutter rolling direction of the scanning camera, under the rolling shutter exposure mode, the scanning camera can perform a parallel exposure for next frame of image before the exposure of a former frame of image is finished, and the computing device can splice each frame of image which is subjected to continuous exposure to form a complete digital section. By means of the technical scheme, the uniform motion speed of the section sample can be improved, simultaneously the motion blurring caused by sample motion during exposure of the scanning camera can be reduced, the image acquisition speed is improved, and the image acquired by the scanning camera is clear and stable.