The invention discloses a bacterial colony automatic detection method, belonging to the fields of biomedicine image processing, environment monitoring and the like. The method comprises the following steps:inputting bacterial colony images; carrying out image gradation processing and pre-processing on the bacterial colony images, and acquiring the processed bacterial colony images; carrying out ideal bacterial colony image reconstruction according to the processed bacterial colony images; and post-processing the ideal bacterial colony images, and detecting the bacterial colonies, wherein, when the bacterial colony images are acquired at different conditions, the input bacterial colony images are converted into the ideal bacterial colony images by eliminating illumination deviation, and the ideal bacterial colony images are subject to post-processing, thus the bacterial colonies are detected. The bacterial colony automatic detection method does not rely on a specific image acquiring device, bacterial colony types and external environmental conditions, and the image segmentation and bacterial colony extracting processes also do not rely on experimental threshold value or prior knowledge, Thus the bacterial colony automatic detection method has the advantages that the universality is high, the application range is enlarged; and large-scale experiments prove the accuracy and precision of the bacterial colony automatic detection method.