A stochastic model of nanocrystals (NC) aggregation governing mobilities both of individual nanocrystals and its clusters is developed. The influence of the model parameters on the NC morphology is considered and an analysis is made of the applicability of the model to describe various real physical systems. The model is applied to simulate an aggregation of cadmium sulfide nanocrystals upon evaporation of the Langmuir–Blodgett matrix and as a result a comparison of simulations and experimental results is carried out. We give a comprehensive analysis of the patterns simulated by the model, and study an influence of the surrounding medium (solvent) on the aggregation processes. This system is a typical example from real life and is noteworthy in that the morphology of NC after evaporation of the matrix cannot be described exactly by a model based only on the motion of individual nanocrystals or by a cluster–cluster aggregation model.