Module can not only affect the integration of network functions, but also contribute to understand the characteristics of local connections in the network. However, the connection between nodes in the network changes with the passage of time, and the module structure changes accordingly. To overcome this drawback, we propose a method of applying weighted clustering ensemble to partition multilayer brain functional networks into modules. Firstly, k-means clustering is adopted to carry out base clustering for a certain layer of functional network for several times, and each clustering is corresponding to a subordinate matrix and a similarity matrix. Then clustering validity index is used to assess each partitioning and the assessed values are taken as the weights of similarity matrix. Finally, the weighted similarity matrix is partitioned by means of fuzzy C-means clustering, and the results are evaluated by modularity function to obtain the optimal partitioned modules. Experimental results show that the effect of module partitioning resulting from weighted clustering ensemble is better than that of other comparable methods. The proposed framework could be promising to analyze the differences between corresponding modules of patients with Alzheimer’s disease and normal people, so as to better understanding some dynamical pathological changes in brain connectome of patients.