A novel watershed algorithm using mountain areas simulation method to segment the field emission images was proposed for the first time. In the algorithm, field emission sites in the images are compared to many mountaintops. The small fluctuations in the mountains are first erased by filling method. And then the traditional watershed transform is applied to get the mountain areas roughly. At last the parameters of the relative height needed for a mountaintop are used to segment the field emission sites by a series image process of dilation and comparation. This segmentation method is very easy to be accomplished in MATLAB and have high efficiency. Results show that the improved watershed algorithm is feasible in analyzing field emission properties and some other applications.