A method for labeling connected components and a computer system using the method are provided. With the method, during a process of scanning an image for the first time, each object pixel in the image is assigned a temporary label, and a relationship between each temporary label and a representative label is established after the completion of the process of scanning the image for the first time. Thereafter, the temporary label of each object pixel is replaced by the corresponding representative label during a process of scanning the image for the second time. As a result, the labeling of the connected components can be accomplished by only scanning the image twice such that the efficiency of labeling the connected components can be significantly improved.