It was researched interaction modeling in a heterogeneous population and development of methodology for calculating the ABM modeling. Was obtained formation model of interaction in a heterogeneous population containing distribution agents in six clusters, its mathematical model and application of mathematical model to research the process of crystallization. Also, results were obtained in applying the crystallization process. Both analytical and numerical approaches, research-stochastic interactions in complex heterogeneous successfully applied and did describe the quality of the results obtained both by the interaction process in a heterogeneous population containing 6 the distribution of clusters, as well as the crystallization process using the mathematical model shown analytically that there are three different states (cluster liquid interface between the cluster and liquid) with four possible distributions of these states.