To overcome the limitation of the traditional FCM that only can deal with samples of clusters with the similar size, this paper proposed a fuzzy clustering algorithm with effectiveness factor. The algorithm prevented some clusters with small samples from being annexed by those with large samples. In this paper, by the proof of update rules for degree of membership, the objective function and rules for clustering center replacement and experiments with FCMef and FCM, the adding of effectiveness factor can improve the clustering effect obviously. While the value of the effectiveness factor increases, the clustering effect can be improved in many instances.