Abstract The formation of large Morse atomic clusters is a complex and time-consuming task, especially when the cluster stiffness equals 14. Currently, optimal cluster conformations are known for sizes up to 240 atoms. The article proposes a parallel stochastic algorithm for the structural evolution of Morse clusters, which makes it possible to find the optimal conformations of large atomic clusters. A significant number of problems associated with the complexity of the task are resolved using the proposed algorithm for optimizing the cluster structure. The results of optimization of Morse clusters for N> 240 are given.