Design of district metered areas(DMAs) in water distribution system was performed based on complex network spectral clustering and graph theory. First the number of DMAs was determined, and graph weighted adjacency matrix and Laplacian matrix were established. Then k-way spectral clustering algorithm was used to discover the optimal clusters hidden behind eigenvectors of Laplacian matrix, leading to the best layout of DMAs using genetic algorithm and K-means. PageRank and shortest path algorithm were adopted to ascertain the location of meters in DMAs and valves between DMAs to achieve the optimal design of DMAs eventually. And a real water distribution system was tested and the results showed that the proposed method was effective in DMAs design.