Cell dynamics simulation (CDS) is a very promising approach to model dynamic processes in block copolymer systems at the mesoscale level. It is difficult to implement a real time and experimental‐scale simulation with traditional serial algorithms because of the expensive computation. A parallel, spatial decomposition‐based algorithm for large‐scale CDS is proposed. With the efficient strategy of domain decomposition and the fast method of neighbouring points location, we greatly reduce the calculating and communicating cost. The numerical results indicate that the proposed parallel algorithm can provide an efficient procedure for computer simulation of block copolymer systems of experimental size.