Studies of the last decades have brought the results of modern natural science into technology of composite materials of the widest range. The methods of percolation theory have become constructive tools for studying the structure of composites, for the purposeful creation of materials with desired properties. In this paper, a computer model of the processes of self‐organization of percolation clusters has been created. The model considers such problems with self‐organization, in which the properties of a percolation cluster are also determined by the history of the system's development. To study the structure and properties of such systems, a three‐dimensional continuum percolation problem with interacting elements is solved in the model. Iterative algorithms for the motion and interaction of particles and clusters, leading to the formation of percolation systems, have been developed. Their structure and properties have been studied, a number of standard parameters have been calculated, and the dependence of the structure and properties of clusters on the rate of system generation, degree of self‐organization, and characteristic values of the correlation length has been studied; analytical dependences of a number of parameters of percolation systems are obtained.