Abstract The paper suggests a unified stochastic method in order to simulate multi-agent interactions in heterogeneous complex systems. This approach (which appears phenomenological if it is not agent-based) can describe precisely the average outcomes of multiple agent-based computations (where there is a lack of probabilistic insight). The recent discussions about the gap between agent-based computational models (ABM) and stochastic analytical models have stimulated the present research (Feng et al., 2012  and Kononovicius and Gontis, 2013 ). In general, agent-based modeling is currently a technique widely used to simulate complex systems in computer science and social sciences. The present developments in the physics of complex systems, in particular the structural relaxation of supercooled liquids and glasses, are also discussed by using such probabilistic approach. It is possible to depict the impact of interface between the nucleus considered as a cluster of a certain number of molecules and the liquid phase for the enhancement of the overall nucleation process. In this study, a useful aggregation procedure for representing the three-dimensional distribution of states and a general equation that describes clustering process among interacting agents in heterogeneous populations are proposed.