At present, screen image compression techniques are mostly designed for computer desktop, and there is still much room for improvement of the image compression quality and compression ratio, etc. when applied to scientific instruments workstation screen image. In order to solve such problems, this paper puts forward a kind of compression method applicable to scientific instruments workstation screen image. Firstly, get the statistics information and analysis of the color value of screen image, and determining its distribution characteristics, and construct a 256-color palette for color quantization through merging the similar color of the window title bar of programs to reduce the number of color types. In addition, use the image layering and improved run-length coding techniques to enhance the continuity of the same color pixels of the background image and the image compression ratio. Test results show that the algorithm applied to scientific instruments workstation screen image has significant advantages in image coding speed, compression ratio and mean square signal to noise ratio of the output image.