The invention provides a method and system for processing a medical image. The method comprises the following steps that the image is read and displayed, the image is zoomed and rotated, negative film effect processing is conducted on the image, the image is cut, the grey level of the image is transformed, the contrast ratio of the image is increased, the image is displayed in the mode of a histogram, the histogram of the image is equalized, noise of the image is eliminated, the edges of the image are detected, the image is smoothed, and the image is sharpened. The system comprises a central processing unit, an image collecting module, an image processing module, a display module and a storage module, wherein the image collecting module, the image processing module, the display module and the storage module are respectively connected with the central processing unit. According to the method and system for processing the medical image, the medical image is read in and displayed, so that a series of processing is conducted on the medical image, the image processing technologies are fully used for effectively improving the image quality, diagnosis and treatment which are relative to the state of an illness and conducted by a doctor are facilitated, and the phenomena of missed diagnosis and misdiagnosis are avoided.